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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

This list is also available as an RSS feed (devel branch), and RSS feed (release branch)

Package: lefser
Commit: f1bea8cd98805249bf0dd29c83cf903a40953558
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:49:00 -0500
Commit message:

 version bump 1.21.5

Package: lefser
Commit: 447161c640222da12697a44d4e843c5a9b7b1d45
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:46:02 -0500
Commit message:

 fix formatting lefser.R

- clean up spacing in example

Package: lefser
Commit: 4c77e9ad9f8982a0a9f17166048feca9050f0a8e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:39:31 -0500
Commit message:

 update NEWS.md

Package: lefser
Commit: 15bf801b8e12d7587f7fbadad0efc1970cd1f12e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:27:33 -0500
Commit message:

 version bump 1.21.4

Package: lefser
Commit: b32f3b7cc73e8f841774fec971e4df7f59dcaf38
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:27:28 -0500
Commit message:

 update NEWS.md

Package: lefser
Commit: dcc410ad30a0c90087176a6bb5d45ad70dca9d28
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:25:10 -0500
Commit message:

 version bump 1.21.3

Package: lefser
Commit: 4e485d0bfd46c110ebf4a54a3f308aff7d4eb546
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 13:22:23 -0500
Commit message:

 compare data[, "class"] with actual value in classes

Package: rhdf5
Commit: 1da9c5800a02cbc48c8e3ee8ba9ae3f0b31548f7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 18:09:01 +0100
Commit message:

 Fix more rchk issues

Package: rhdf5
Commit: a85f9df53f32094919ed3d7395ffb3c5176bf56e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 17:47:28 +0100
Commit message:

 Use more friendly name for rchk workflow

Package: rhdf5
Commit: 87879d52c3cdf308599ac4b161491a03ec3e8769
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 17:37:04 +0100
Commit message:

 Try making all PROTECT/UNPROTECT analyzable by rchk

Package: rhdf5
Commit: ed9c07e6dc111c4e3f9b0f613c3c17c18745e1e9
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 16:55:47 +0100
Commit message:

 Fix rchk workflow

Package: rhdf5
Commit: bd5d9908ea0432e26cd5b4fd8a9d8ddb5e391b39
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 14:37:10 +0100
Commit message:

 Trigger rchk on self change

Package: rhdf5
Commit: 8ea3659a91a7803b8cd63aad883aa3fc9f218571
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 14:35:40 +0100
Commit message:

 Create dedicated rchk workflow

Package: rhdf5
Commit: bbc742c08bc1479d09353a3aa7e31fd6123178e5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 13:23:27 +0100
Commit message:

 Use seq_along() instad of seq_len(length())

Package: rhdf5
Commit: cbf3fd108722e860d5e0ea3539956c2f776ae500
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 13:19:31 +0100
Commit message:

 Use <- for assignments

For consistency across the codebase

Package: rhdf5
Commit: 523cf14a584e2349519e51a423bc0de61d2afa91
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-14 13:15:36 +0100
Commit message:

 Fix typo in env var name

Package: GloScope
Commit: a896d24d5c64213016ca0e634d8d6dcb7cb931e1
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2025-11-13 04:24:34 -0800
Commit message:

 bump version and NEWS

Package: lefser
Commit: 7c8bfd3ba18ec9b6ae647466f74990ea7494e497
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 10:50:37 -0500
Commit message:

 version bump 1.21.2

Package: lefser
Commit: 39d14c43e1ce6af39366a5d57b4a395b356cb374
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 10:49:57 -0500
Commit message:

 remove whitespace

Package: lefser
Commit: 1bc2b02526c2fe603be59115a37f561e7eb9e277
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 10:48:26 -0500
Commit message:

 clean up formatting

Package: lefser
Commit: 1ea2c4f13f6081491d2368fe5bbeeb77dbb1d1f7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 10:44:21 -0500
Commit message:

 import case_when and relocate from dplyr

Package: lefser
Commit: cfd85bf2a9f262654b0aa1d8ffb9711aa8842bb8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 10:42:54 -0500
Commit message:

 don't import %>%

Package: lefser
Commit: 6c31156ced8511380d921112c098a6cc232bedc5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-14 10:42:18 -0500
Commit message:

 avoid 1:n sequences

Package: Aerith
Commit: 45834958f08c334a995afedf6181e7171c00f08c
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-12 03:06:43 -0600
Commit message:

 fix mzml-reading vignettes

Package: Aerith
Commit: 581770efe82a28e9d8802b82a6cf85f991b8a683
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-11 23:18:13 -0600
Commit message:

 bump version

Package: Aerith
Commit: f513a91306a89aa75b5796b4ac1121ff5d59b1bb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-11 22:31:33 -0600
Commit message:

 bump version

Package: Aerith
Commit: 8e596324f1014e6e92253c0fe4b04e221cd7fc34
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-11 22:29:07 -0600
Commit message:

 reduce size of demo.mzML

Package: Aerith
Commit: 632b2eb4cbb9ea131e2a551fa9a7c9cb95ae5474
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-11 20:49:02 -0600
Commit message:

 reduce github repo size, deleting png/logo.psd, zip demo.FT1

Package: Aerith
Commit: c93373e6895d3e67d0a660a179d6a22f5104dc7a
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 17:09:34 -0600
Commit message:

 bump version

Package: Aerith
Commit: d68a889efe4cf6d3f5b6f8b6c190a5e0dc238d68
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 17:02:43 -0600
Commit message:

 fix citation

Package: Aerith
Commit: 1d4492d2194e9f3ff1ac3a2e7373222a9966ff4b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 12:20:21 -0600
Commit message:

 add citation

Package: Aerith
Commit: cbd9dfd37d5580f26b1766e05e735224a5039dc5
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:52:24 -0600
Commit message:

 merge from upstream

Package: Aerith
Commit: 179de722fb6a13a6477dca9cbca909c993fb8ea7
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:45:50 -0600
Commit message:

 revise to 4 spaces for line indents, add citation

Package: Aerith
Commit: b56a249309b202716944f1693a91db2cdbfef956
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 10:36:18 -0600
Commit message:

 refine readme.md under windows, replace @ to slot(), add demo for precursor_peak_calculator_DIY_averagine

Package: Aerith
Commit: d8091e9c062ee2ff0df6e7fc86c12a1dd1408daa
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-28 11:35:29 -0500
Commit message:

 fix missing \value sections

Package: Aerith
Commit: 417bc2e6edc04847b34ef6b51d3238e22461a3c0
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-27 21:12:42 -0500
Commit message:

 fix missing \value sections

Package: Aerith
Commit: 49bced2eea57bb63d690e587d7efdd756c56112c
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-27 02:26:16 -0500
Commit message:

 fix .git files limit error, and Empty or missing \value sections warning

Package: Aerith
Commit: c36706204dcd29563e4b842ac6192571ee375f5f
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-23 13:41:31 -0500
Commit message:

 fix compile error on mac

Package: Aerith
Commit: e2ff51fa767c673793d876366193912f7ad86309
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 03:34:58 -0500
Commit message:

 bump version

Package: Aerith
Commit: 9329c47fc7942858b63968e30b8351051d18fff7
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 00:10:27 -0500
Commit message:

 add demos to some rcpp function, optimize vignettes

Package: Aerith
Commit: b06ebaf66ebd7d30b7afcbe421326eb234436947
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-10 02:50:29 -0500
Commit message:

 bump version

Package: Aerith
Commit: b18dbc0418c53e9ffd8790f770fe5d65b168712d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-10 02:14:18 -0500
Commit message:

 revise document of plot-AAspectra

Package: Aerith
Commit: ff8c93a0f588fd53500cc30d3b197fc6eefe4463
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 21:08:54 -0500
Commit message:

 Remove configure.sh from tracking

Package: Aerith
Commit: e0b09b3b128df23f52ba84fca7a87602f72788ec
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 20:56:59 -0500
Commit message:

 revise document of plotAAspectra.R and plotProteinSipPct.R

Package: Aerith
Commit: 20f745f780c295b1b4a884a6582ce27030039d76
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 03:08:12 -0500
Commit message:

 Stop tracking vignettes/.gitignore

Package: Aerith
Commit: ef0ffaf9ca1caa69b51431d313894bbbc4b62ca9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 03:04:31 -0500
Commit message:

 Stop tracking .vscode

Package: Aerith
Commit: 0b91bc72e6dc33d076b7a282617fe85e15128d47
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 02:59:11 -0500
Commit message:

 Stop tracking .gitignore .Rbuildignore

Package: Aerith
Commit: db0647b6417bc005b16503c55ad74cc146e6dbb8
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-08 22:20:21 -0500
Commit message:

 change tests using built-in demo files

Package: Aerith
Commit: 4be8164b87d6a3c90911ee74e7da3684e6dad6a1
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-08 00:19:45 -0500
Commit message:

 update Score-function-test-of-PSM.Rmd, Theoretic-spectra-generation-of-SIP-labeled-compound.Rmd, Theoretic-spectra-generation-of-SIP-labeled-peptide.Rmd, Visualization-of-SIP-proteomic-result.Rmd. Remove eval=FALSE chunks

Package: Aerith
Commit: 0bef766c91cfb1f18e9a09a31064691289cbc882
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-04 22:41:57 -0500
Commit message:

 update Aerith.Rmd, Input-data-format.Rmd, PSM-annotation-and-visualization.Rmd. Remove eval=FALSE chunks

Package: Aerith
Commit: 7a59c8fac885e828ee8f233fa83c3e16d21d32a9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-04 02:14:33 -0500
Commit message:

 add filterIsotopicPeaksTopN, set OMP_STACKSIZE = "16M" when init, add parameters for plotMolecularIsotopes

Package: Aerith
Commit: fda5360f28157ea853bad715ffe9aea43019655d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-16 20:26:39 -0500
Commit message:

 Merge branch 'main' into dev

Package: Aerith
Commit: a6f58c1a415ae9831019d9a48a2cd3f44b465496
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-15 21:48:55 -0500
Commit message:

 bump version

Package: Aerith
Commit: 400442363dbbcaa7ada61ab00edb98cee856091e
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-15 21:39:12 -0500
Commit message:

 fix cran warnings

Package: Aerith
Commit: 7da885807807cf112af22d612be09c669489ecbb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:19:30 -0500
Commit message:

 bump version

Package: Aerith
Commit: c9f9c6c80e85b1c2a268384d8bc792bf0a1db8ef
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:13:21 -0500
Commit message:

 Merge updates for .gitignore, plotPSMs.R, readScans.cpp, and test_scorePSM.R from dev branch for fix R CMD check error

Package: Aerith
Commit: 6f12097ba9c2771e94ef6fe5128078f6464c01c6
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 01:26:32 -0500
Commit message:

 fix R CMD check error

Package: Aerith
Commit: 24fb2bce328b2ac5894b9ef5274eff6f14a3bbb1
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 21:03:37 -0500
Commit message:

 Merge branch 'dev'

Package: Aerith
Commit: dea3212b755f0edec5a84f34862fc1c9c52179ce
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 20:58:52 -0500
Commit message:

 revise vignettes

Package: Aerith
Commit: ce0fdcbf2f1bc72b3dad36bd74c6ee24f965b79e
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 19:37:52 -0500
Commit message:

 remove extdata

Package: Aerith
Commit: 2f69074fe72af2c7a6cab79ca0d1d09d48c37878
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 19:30:19 -0500
Commit message:

 revise vignette from dependent on rmd folder to inst/extdata folder

Package: Aerith
Commit: 18689bc8b93ae98f0bb995d32ee6ccd74f235a17
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-27 00:12:48 -0500
Commit message:

 Update DESCRIPTION with GPL-3.0

Package: Aerith
Commit: 83d6cc78d0dd68338b403d796a44481b60debc6c
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-27 00:08:39 -0500
Commit message:

 Update LICENSE.md to markdown style

Package: Aerith
Commit: cde9912a4c29a30b549c5475e83ae33311bd9126
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-26 23:58:23 -0500
Commit message:

 Create LICENSE.md

Package: Aerith
Commit: 7ec40c6bfb5075ad434ea5148e16627ce76a4f25
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-26 23:50:59 -0500
Commit message:

 version bump

Package: Aerith
Commit: 4193f4fc362b930278dcd558ced9e799479cad44
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-26 03:32:46 -0500
Commit message:

 fix file path error of plotPSMs function on windows

Package: Aerith
Commit: a00d3b76d629aa7802aa9aaae97fc6dc76a4e4e9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-26 01:22:35 -0500
Commit message:

 Add documentation for the exported functions recommended by Bioconductor.

Package: Aerith
Commit: 0c18dbdf322807c0487dc12846b8f31017213e98
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-21 12:34:01 -0500
Commit message:

 fix warning form BiocCheck::BiocCheck

Package: Aerith
Commit: 2ff70ddd4c39bf25ad45225ae108757c11ae4f1d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-21 03:48:21 -0500
Commit message:

 revise for bioconductor submitting

Package: Aerith
Commit: dbebf07d2cf015d9c5c41c4331f6554405ce52ab
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-05 00:54:50 -0500
Commit message:

 add link parameter for openmp on windows, add suggesting import of mzR and MSnbase

Package: Aerith
Commit: b9017dd8287d30df6f67fa5f3dafd88ccd29a014
Author: xyz1396 <1074082710@qq.com>
Date: 2025-04-16 12:18:51 -0500
Commit message:

 optimize readme

Package: Aerith
Commit: 6c2f1adc802c912d14302b63462351dada35f641
Author: xyz1396 <1074082710@qq.com>
Date: 2025-04-16 02:27:37 -0500
Commit message:

 add simplified calculation of WDPscore; revise spectral entropy to consider all peak intensity in real scan

Package: Aerith
Commit: cb2dda9696a2444d4450f177a4d3715afa333c60
Author: xyz1396 <1074082710@qq.com>
Date: 2025-03-11 02:23:32 -0500
Commit message:

 add vignettes for score function and PSMs results visual

Package: Aerith
Commit: 0ba6e6923556e1ac4ce68212cbb187e427fc567c
Author: xyz1396 <1074082710@qq.com>
Date: 2025-02-15 01:43:03 -0600
Commit message:

 vignette of PSM-annotation-and-visualization, add line_width and color setting of function plotAAsectra, add MVH score from myrimatch

Package: Aerith
Commit: c944beef83e835de80c547b49df849abfa6304ab
Author: xyz1396 <1074082710@qq.com>
Date: 2025-01-09 12:36:09 -0600
Commit message:

 add vignettes

Package: Aerith
Commit: 697e8c9876c3feafdda5d117aa73c040c33b25f4
Author: xyz1396 <1074082710@qq.com>
Date: 2024-12-24 20:01:26 -0600
Commit message:

 add .vscode folder in track

Package: Aerith
Commit: 987d7d38ab7cdf00dd87d03796e753473016f9df
Author: xyz1396 <1074082710@qq.com>
Date: 2024-12-20 02:13:00 -0600
Commit message:

 optimize PSM feature extract speed. add mentocarlo and fft isotope peak generate function

Package: Aerith
Commit: 461ce6591c06f5c481da73078fcd68c4cb7c6e47
Author: xyz1396 <1074082710@qq.com>
Date: 2024-11-06 20:02:47 -0600
Commit message:

 refine spe2pepreader, featureextractor, addfunction for reading pepxml file

Package: Aerith
Commit: be711752672ac563f06ce1622138094f90ade444
Author: xyz1396 <1074082710@qq.com>
Date: 2024-08-13 11:42:42 -0500
Commit message:

 add function for PSM isotopic peaks annotation

Package: Aerith
Commit: b16c96477c805283595dd89939f34281abb72dae
Author: xyz1396 <1074082710@qq.com>
Date: 2024-06-10 23:37:31 -0500
Commit message:

 delet test.cpp

Package: Aerith
Commit: efd79b033dd8eabdb8706a2db8b32d3d46c469d2
Author: xyz1396 <1074082710@qq.com>
Date: 2024-06-10 23:24:46 -0500
Commit message:

 add  and 
 </pre>
    </div>
  
    
      Package: Aerith

      Commit: 091072fc0d5af08aac7ac3641b2902c118a8bcf1

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-06-10 23:16:27 -0500

      Commit message:


	  
		 extract other features from MS1 level of sipros spe2pep file
 
    
  
    
      Package: Aerith

      Commit: 68ff69194849d9fa7249021d062256382f9f2f12

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-05-09 00:03:46 -0500

      Commit message:


	  
		 add extract feature function and move to sipros5 spe2pep format with precursor scannumber
 
    
  
    
      Package: Aerith

      Commit: 7976b5aba7439f6e34ee75e98a2d1902e4e70816

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-04-23 00:16:07 -0500

      Commit message:


	  
		 extract isotopic abundance from MS1
 
    
  
    
      Package: Aerith

      Commit: 9eeac800996bd7fcb0f256d3227118e53dae2237

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-04-04 00:19:13 -0500

      Commit message:


	  
		 update to the FT2 file format of Raxport5 and spe2pep format of Sipros 5
 
    
  
    
      Package: Aerith

      Commit: 95742d907e0c0a945d0ea4fd4f8fa8ba8ed65f48

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-01-25 19:19:27 -0600

      Commit message:


	  
		 improve reading ft file performance
 
    
  
    
      Package: Aerith

      Commit: 72b458cc7a04e6e5f915237e4e1d2a4c83509abe

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-11-23 22:22:23 -0600

      Commit message:


	  
		 for reading .Spe2PepFile
 
    
  
    
      Package: Aerith

      Commit: bf0c8654118f7f4bace7c7c2870af0da9dbe8a57

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-04-13 23:25:36 -0500

      Commit message:


	  
		 add denoise function, refine psm plot function
 
    
  
    
      Package: Aerith

      Commit: 25c0c53c63f4c5fc44167329922d40ea5ae8f9bf

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-08 00:10:20 -0600

      Commit message:


	  
		 revise read me again
 
    
  
    
      Package: Aerith

      Commit: 53e6bd493dc5eff70b5041f5d095d2c139d10b22

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-08 00:09:03 -0600

      Commit message:


	  
		 revise read me
 
    
  
    
      Package: Aerith

      Commit: 8d41be5167dd13e089bf47bc69b6f63c1425c285

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-06 23:44:59 -0600

      Commit message:


	  
		 change read me
 
    
  
    
      Package: Aerith

      Commit: cd0dfaa55e96fb2ca7aa11dd07cc3b0efa869802

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-06 23:42:45 -0600

      Commit message:


	  
		 upload files
 
    
  
    
      Package: GBScleanR

      Commit: 6f12fb4beb05c3377f2b5071c8ee1dd47101ab80

      Author:  tomoyukif <f.tomoyuki@okayama-u.ac.jp> 

      Date: 2025-11-14 21:14:30 +0900

      Commit message:


	  
		 Fix a version description in NEWS.md
 
    
  
    
      Package: GBScleanR

      Commit: 7eef28c0d4bea6450d9b9a9ee90a2e8815857fa7

      Author:  tomoyukif <f.tomoyuki@okayama-u.ac.jp> 

      Date: 2025-11-14 21:10:37 +0900

      Commit message:


	  
		 Fix a minor bug in seqOptimize().
 
    
  
    
      Package: rhdf5

      Commit: b55f6b79b298b6960da169dd1f3875d6f764ba66

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-14 11:04:03 +0100

      Commit message:


	  
		 Revert "Balance PROTECT() and UNPROTECT() calls"

This reverts commit 131f0a026764f2d3f375fe2fe554b608ab50d0dd.
 
    
  
    
      Package: igblastr

      Commit: fda6d209bb8a69d3048b7cbe379f7ea069463843

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-13 15:24:22 -0800

      Commit message:


	  
		 more tweaks to R-CMD-check-bioc workflow
 
    
  
    
      Package: igblastr

      Commit: 5dc7e590e4c34b988c019019c976aedc9c0ab502

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-13 15:20:04 -0800

      Commit message:


	  
		 more simplifications of R-CMD-check-bioc workflow
 
    
  
    
      Package: igblastr

      Commit: 5def77f8296f3f825afe367c7b7af67fe1148218

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-13 15:00:58 -0800

      Commit message:


	  
		 update R/BioC versions for GitHub actions
 
    
  
    
      Package: VisiumIO

      Commit: 24aec3bfb03899e14221899ceff064787bd486af

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-13 16:42:41 -0500

      Commit message:


	  
		 version bump 1.7.2
 
    
  
    
      Package: VisiumIO

      Commit: 840da0b803386d68598bd96a26c759ad757cf472

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-13 16:42:13 -0500

      Commit message:


	  
		 update NEWS.md
 
    
  
    
      Package: VisiumIO

      Commit: 0e8146615cc982cc59f2a7205ecd02cb03391027

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-13 16:40:14 -0500

      Commit message:


	  
		 fix sample_id typo in TENxVisium call
 
    
  
    
      Package: GOfan

      Commit: 49baf7cfcc63033c660da310bbfeea722de1e245

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-11-13 16:31:01 -0500

      Commit message:


	  
		 add returning value section for geom_sunburst.Rd
 
    
  
    
      Package: VisiumIO

      Commit: 290a871fe95139531a790f292ba8ef4eb3924bb7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-13 16:30:41 -0500

      Commit message:


	  
		 version bump 1.7.1
 
    
  
    
      Package: VisiumIO

      Commit: ad6658ead0226067f7768f9bad6eeda2ae2025eb

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-13 16:29:21 -0500

      Commit message:


	  
		 update NEWS.md
 
    
  
    
      Package: VisiumIO

      Commit: 69805ca1746e2f523cfe615d2d4765135da87906

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-13 16:26:55 -0500

      Commit message:


	  
		 simplify logic and rely on previous path existence check
 
    
  
    
      Package: OmnipathR

      Commit: a0e107e7823bf8f80ad70721ba90f4f21c41045e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-13 19:47:20 +0100

      Commit message:


	  
		 Bump version: 3.19.0 → 3.19.1
 
    
  
    
      Package: OmnipathR

      Commit: 8eaad5171deea88dcc21e36b575663a3862e014d

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-13 19:46:58 +0100

      Commit message:


	  
		 applied BioC version bump to `bump2version`
 
    
  
    
      Package: OmnipathR

      Commit: 05d20bf178eed89e2f5fa62bdaf4e4a38d270345

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-13 19:45:46 +0100

      Commit message:


	  
		 Merge branch 'devel' of git.bioconductor.org:packages/OmnipathR
 
    
  
    
      Package: OmnipathR

      Commit: 5e112d772f7fb20c778be915089ff0d673a37205

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-13 19:45:35 +0100

      Commit message:


	  
		 `recon3d`, `cosmos`: added missing varible declarations
 
    
  
    
      Package: OmnipathR

      Commit: fb423f4d729975bc73a3656f3e6296c277ac345e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-10-29 17:29:34 +0100

      Commit message:


	  
		 typo in `recon3d.R` in `slow_doctest` calls
 
    
  
    
      Package: DESeq2

      Commit: 4dda123d0f1da040ea1a66f591559d534bd30bbd

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-13 12:55:33 -0500

      Commit message:


	  
		 version bump and thanks for #123
 
    
  
    
      Package: DESeq2

      Commit: 6acb0dcdf12f2f3cdb56e4bcefe356658af10e2b

      Author:  Michael Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-13 12:53:26 -0500

      Commit message:


	  
		 Merge pull request #123 from Bisaloo/partial-matching

Remove some instances of partial matching 
    
  
    
      Package: DESeq2

      Commit: 2bc293c8da38e41846a4472fe522906b004aeef2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-13 17:33:04 +0100

      Commit message:


	  
		 Remove some instances of partial matching
 
    
  
    
      Package: rigvf

      Commit: d491bcc81c6e99fa9db8c0917f51ba0a0946418a

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-13 10:53:32 -0500

      Commit message:


	  
		 version bump
 
    
  
    
      Package: rigvf

      Commit: 281c98970c1f027a165531b58db96a35219537bf

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-13 10:45:00 -0500

      Commit message:


	  
		 fixing to address api url change
 
    
  
    
      Package: epiregulon

      Commit: 9dec0f9751cb6c058b5774fac61d8e5194061182

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-13 15:16:00 +0000

      Commit message:


	  
		 message formatting
 
    
  
    
      Package: epiregulon

      Commit: cedbf83d69c024b624c9e29ac97384b1d8c8f43e

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-10 11:04:56 +0000

      Commit message:


	  
		 cell aggregation
 
    
  
    
      Package: epiregulon

      Commit: 9fcc8963ae1af1dc061b0ec49ad3b930e17a1bbd

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-09 18:10:16 +0000

      Commit message:


	  
		 code cleaning
 
    
  
    
      Package: epiregulon

      Commit: aef94e88ba7b0bd94d388ce7c9dbf711a0c8ded1

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-09 18:10:00 +0000

      Commit message:


	  
		 clusters and .create_metacells unit tests
 
    
  
    
      Package: epiregulon

      Commit: fb4b461c73bee5e0466a562699fc314c6d38b951

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-09 17:52:51 +0000

      Commit message:


	  
		 warning formatting
 
    
  
    
      Package: epiregulon

      Commit: 66017455668f8beeb07134638d7927bfe7a403cb

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-04 10:01:21 +0000

      Commit message:


	  
		 typo
 
    
  
    
      Package: epiregulon

      Commit: 137e07fb39b175f50d59d2e1c4a7e67c2e69f050

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-04 09:46:28 +0000

      Commit message:


	  
		 calculate means when cells are aggregated
 
    
  
    
      Package: epiregulon

      Commit: 4a5858cadd1d449747faccb0a4fa05808378457e

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-04 09:26:36 +0000

      Commit message:


	  
		 fixing bug related to a missing sce
 
    
  
    
      Package: epiregulon

      Commit: 0695be69f786b95cc59e935583dbae9944663040

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-04 09:04:54 +0000

      Commit message:


	  
		 documentation correction
 
    
  
    
      Package: epiregulon

      Commit: 17cd6842d2e59a5e937bf55ef1c5cb3507634029

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-03 14:43:28 +0000

      Commit message:


	  
		 v2.1.2
 
    
  
    
      Package: epiregulon

      Commit: 393bab567c83f19fa55600d9706ef0b3c261be86

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-03 10:46:33 +0000

      Commit message:


	  
		 formatting message
 
    
  
    
      Package: epiregulon

      Commit: f4e023255ba67858552e9afb9ffd797a78ab49cb

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-03 10:41:15 +0000

      Commit message:


	  
		 correct condition
 
    
  
    
      Package: epiregulon

      Commit: f7f6e2e507f5c27f263fe1575bac6c01d5d44826

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-03 06:38:35 +0000

      Commit message:


	  
		 v2.1.1
 
    
  
    
      Package: epiregulon

      Commit: f384452173df7d96bae4b991f5221d393cbe3b09

      Author:  TomVuod <tomasz.wlodarczyk@contractors.roche.com> 

      Date: 2025-11-02 12:03:05 +0000

      Commit message:


	  
		 correct warning and error message
 
    
  
    
      Package: Rarr

      Commit: 99b253a935a20241fe83ad6a1cc038144bae69ac

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-13 10:47:34 +0100

      Commit message:


	  
		 Add tests for ZarrArray()
 
    
  
    
      Package: Rarr

      Commit: 2dfc651f330433e919454832f1b20e6df684e6e0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-11 15:54:58 +0100

      Commit message:


	  
		 Add writing benchmarks for new data types
 
    
  
    
      Package: Rarr

      Commit: fc524368faa281751a6c8b4f219133f31cd5e42f

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 11:33:28 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: Rarr

      Commit: d18e8b11e48da5abfcac908d143aa5aeb185cda3

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 11:33:11 +0100

      Commit message:


	  
		 Mention zstd change in NEWS
 
    
  
    
      Package: Rarr

      Commit: dd3a21ec220969977980e9e0a1837998e3e8b8e4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 11:21:04 +0100

      Commit message:


	  
		 Make type handling and conversion more robust
 
    
  
    
      Package: Rarr

      Commit: c615f295796e078b40c19e395ee2820f70d6f9e0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-07 19:47:58 +0100

      Commit message:


	  
		 Guess buffer size when decompressing zstd
 
    
  
    
      Package: Rarr

      Commit: 049a638df6588ce2d826f1dfa059773da14d670d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-07 19:46:31 +0100

      Commit message:


	  
		 Add test for #20
 
    
  
    
      Package: Rarr

      Commit: 3f7d07564339645c4af71f2a5dd08db0069bc2d5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-08 11:32:25 +0100

      Commit message:


	  
		 Remove covr from dependencies
 
    
  
    
      Package: Rarr

      Commit: e9e30392d932858768753e05ecc20e404b5fc2d1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-08 11:31:44 +0100

      Commit message:


	  
		 Rbuildignore .lintr config file
 
    
  
    
      Package: igblastr

      Commit: d706717a91a8d69faa3513f0c6754610dd2e1df4

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-13 02:19:20 -0800

      Commit message:


	  
		 Add 'loci' argument to install_IMGT_germline_db()

This lets the user control what loci they want to include in the
germline db. Documentation and unit tests to follow.
 
    
  
    
      Package: rhdf5

      Commit: afaff0e592fb4165eaf0f53ccec31180a93dea59

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 16:49:35 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: rhdf5

      Commit: 64cc59f999bb8f3ae2e343daf39024d97cc93a16

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 17:11:53 +0100

      Commit message:


	  
		 Add NEWS item about h5ls() hint
 
    
  
    
      Package: rhdf5

      Commit: 9e608518d83d3cbc2c03a1038a401abdea7c7295

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 16:31:39 +0100

      Commit message:


	  
		 Add message also when name is missing
 
    
  
    
      Package: rhdf5

      Commit: fd32d769b71cd31e1e583e3f0b6d38687500a892

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 17:09:46 +0200

      Commit message:


	  
		 Add h5ls() hint in the docs as well
 
    
  
    
      Package: rhdf5

      Commit: 33aa8d0e745a2bd0f0b07677d92e1983cbae59f5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 16:21:27 +0200

      Commit message:


	  
		 Add hint to use h5ls() for unknown object
 
    
  
    
      Package: rhdf5

      Commit: 10cce3ffa4baf3b0cd48542f252c16cab51fcdb6

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-13 10:39:23 +0100

      Commit message:


	  
		 Delete .covrignore

Since we want to also see coverage of the C code 
    
  
    
      Package: rhdf5

      Commit: 0bb291bb73d8eda39ef107cd6f01b091ca9b76d6

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 15:46:59 +0100

      Commit message:


	  
		 Trigger coverage workflow on devel
 
    
  
    
      Package: rhdf5

      Commit: 76801e9bf41e355855dc060c04ab5b85024ebfe8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 15:44:43 +0100

      Commit message:


	  
		 Add manual trigger to test-coverage workflow
 
    
  
    
      Package: rhdf5

      Commit: d7e682847247af56edeb45766979bdacbd5792a4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 15:37:59 +0100

      Commit message:


	  
		 Document internal changes
 
    
  
    
      Package: rhdf5

      Commit: 033dd9845c8acec98ff0d3be434e6d5e7a125398

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-12 15:37:44 +0100

      Commit message:


	  
		 Use upstream test-coverage workflow
 
    
  
    
      Package: rhdf5

      Commit: 1c8419c750e3fac929a81d5356e133f100ce5ff5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 22:32:03 +0100

      Commit message:


	  
		 Run devtools::document()
 
    
  
    
      Package: rhdf5

      Commit: 1884c7ea7ef2d929900eaac3476de566aed53b4c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 22:30:52 +0100

      Commit message:


	  
		 Fix typos
 
    
  
    
      Package: ClusterGVis

      Commit: 15fc47048540b2bc41df2ee539d5d4de54b68ce3

      Author:  junjunlab <1138976957@qq.com> 

      Date: 2025-11-13 09:39:49 +0800

      Commit message:


	  
		 revision 0.99.9 for bioconductor
 
    
  
    
      Package: ClusterGVis

      Commit: e3640c06ff0788abb7318c4c186e6c6bcc72301d

      Author:  junjunlab <1138976957@qq.com> 

      Date: 2025-11-13 09:04:22 +0800

      Commit message:


	  
		 revision 0.99.8 for bioconductor
 
    
  
    
      Package: mspms

      Commit: 20f2c4b7cc8b3408474198ff70570caaa93b7ce3

      Author:  Charlie Bayne <baynec2@gmail.com> 

      Date: 2025-11-12 15:03:42 -0800

      Commit message:


	  
		 update to 1.3.1
 
    
  
    
      Package: mspms

      Commit: 0f72c9d18381ed3eb0c1e37a2c1c653311bd9a2e

      Author:  Charlie Bayne <baynec2@gmail.com> 

      Date: 2025-11-12 15:01:33 -0800

      Commit message:


	  
		 Merge branch 'devel' of git.bioconductor.org:packages/mspms
 
    
  
    
      Package: mspms

      Commit: 3d7fbcd8ec8b083c3bf5a40dfd6373c582ac2ad2

      Author:  Charlie Bayne <43388367+baynec2@users.noreply.github.com> 

      Date: 2025-11-12 12:46:17 -0800

      Commit message:


	  
		 Merge pull request #35 from baynec2/BMC-Reviewer-Comments

Bmc reviewer comments 
    
  
    
      Package: mspms

      Commit: e4e87a8c81f09e90b52cdcffbc9649ad00ed7ee8

      Author:  Charlie Bayne <baynec2@gmail.com> 

      Date: 2025-11-12 12:31:00 -0800

      Commit message:


	  
		 Update 1.2.1: minor fixes and improvements per BMC Bioinformatics reviewer feedback.
 
    
  
    
      Package: mspms

      Commit: 1037f72a42ff956cf1991e08f74253f9337cba51

      Author:  Charlie Bayne <baynec2@gmail.com> 

      Date: 2025-11-04 11:01:23 -0800

      Commit message:


	  
		 changes to address reviewer 1 comment 4
 
    
  
    
      Package: mspms

      Commit: cf7409a1c40d54531af02e371215342561bfbfe0

      Author:  Charlie Bayne <baynec2@gmail.com> 

      Date: 2025-05-23 14:43:09 -0700

      Commit message:


	  
		 * Fixed a bug where rownames in the QFeatures object could be misaligned due to a mismatch in the order of colData compared to prepared_data. Fixed by changing the order of the colData to be the order of the prepared data before reading as a QFeatures object

This had an impact on limma statistics where conditions could be misasigned.
 
    
  
    
      Package: mspms

      Commit: e5129fa8c14ce9bf0506d12496ba0b888ae29f7c

      Author:  Charlie Bayne <baynec2@gmail.com> 

      Date: 2025-05-12 11:21:47 -0700

      Commit message:


	  
		 added prepare_diann() to support DIA-NN output.
 
    
  
    
      Package: methyLImp2

      Commit: 579f07b6fdaa9173e0c8f3950a51ed3adb061927

      Author:  annaplaksienko <anna@plaxienko.com> 

      Date: 2025-11-12 18:27:08 +0100

      Commit message:


	  
		 Forgot to delete Rd files
 
    
  
    
      Package: methyLImp2

      Commit: 6ed87500d4884403d95136f770c0ed57175c54aa

      Author:  annaplaksienko <anna@plaxienko.com> 

      Date: 2025-11-12 18:18:08 +0100

      Commit message:


	  
		 Removing internal functions from the manual
 
    
  
    
      Package: plaid

      Commit: f36a0591f762b9f489537fbc469dd9b0db437290

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 17:11:38 +0100

      Commit message:


	  
		 trigger build
 
    
  
    
      Package: plaid

      Commit: 6d890c57b2249fba6ae3801dfaaa86cea24073ad

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 17:09:51 +0100

      Commit message:


	  
		 leave things as before
 
    
  
    
      Package: plaid

      Commit: f91a1ebd3874ef04728318b6c1f837f393f0bf5a

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:58:13 +0100

      Commit message:


	  
		 trigger build
 
    
  
    
      Package: plaid

      Commit: e46ba85db173c042eed193f4d6747dc9dc60e8f8

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:52:43 +0100

      Commit message:


	  
		 bump
 
    
  
    
      Package: Pirat

      Commit: 9e517e49000400cf83576264f986af1a74802c8b

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-12 16:51:34 +0100

      Commit message:


	  
		 Correct last commit
 
    
  
    
      Package: plaid

      Commit: 92723d8dfe973924d1fcf014b8870418010c23dc

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:51:51 +0100

      Commit message:


	  
		 .
 
    
  
    
      Package: plaid

      Commit: 5113ad584ffb61b6e686c6492eb6845848cec158

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:48:07 +0100

      Commit message:


	  
		 indent
 
    
  
    
      Package: plaid

      Commit: 20bddcf1a1aa70ec83526c1dbe036d0441597c91

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:41:53 +0100

      Commit message:


	  
		 correct authors
 
    
  
    
      Package: plaid

      Commit: 97aa187cf7add748683f3205cbe3fbeecb1be097

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:27:41 +0100

      Commit message:


	  
		 bump version
 
    
  
    
      Package: plaid

      Commit: 6a1fb9a36627260123028cf368071724b1f57f82

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-12 16:24:59 +0100

      Commit message:


	  
		 add importFrom
 
    
  
    
      Package: plaid

      Commit: fbb76053040da7eba8900e788a6bb2a4a2495e05

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-12 01:28:46 +0100

      Commit message:


	  
		 Update package title in DESCRIPTION file 
    
  
    
      Package: plaid

      Commit: 42a38287ce77024aa9ffe78a90a5caf6ba0846e1

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 22:13:28 +0100

      Commit message:


	  
		 Update 02_compare-vignette.Rmd 
    
  
    
      Package: plaid

      Commit: 7814043ddb3b6c7fb440a0b6c1c9c83775fdb816

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 21:42:22 +0100

      Commit message:


	  
		 Update 01_plaid-vignette.Rmd 
    
  
    
      Package: plaid

      Commit: d950a56b47fcbdf04a93bfeca7b541976a5b08c6

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 20:29:55 +0100

      Commit message:


	  
		 Fix capitalization in README links and features 
    
  
    
      Package: plaid

      Commit: 2033610ad243897768924fdda85a8a659752049e

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 20:26:26 +0100

      Commit message:


	  
		 Fix README capitalization and warning phrasing

Corrected capitalization and wording in warnings and installation instructions. 
    
  
    
      Package: plaid

      Commit: c06f67abde453bafe3df7d20db2cd775b688e774

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 18:52:35 +0100

      Commit message:


	  
		 add links
 
    
  
    
      Package: plaid

      Commit: c9d835db823ae642047232e48bdd05c47cbabadd

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 15:43:07 +0100

      Commit message:


	  
		 add links to other methods
 
    
  
    
      Package: plaid

      Commit: 8eb71097098dd6cdea0c7e1a07e33da76efa7b52

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 15:42:51 +0100

      Commit message:


	  
		 add links to other methods
 
    
  
    
      Package: plaid

      Commit: 97b68db3938596de5927d70b9be321d7f7644e9b

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 15:40:42 +0100

      Commit message:


	  
		 add links to other methods
 
    
  
    
      Package: plaid

      Commit: 37c469ee43c61a22b0b44384c795f346a128f619

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 15:17:22 +0100

      Commit message:


	  
		 Merge branch 'main' of https://github.com/bigomics/plaid
 
    
  
    
      Package: plaid

      Commit: 81186569c3af5f943ce315f558e280c8b5f184ae

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 15:17:17 +0100

      Commit message:


	  
		 remove files
 
    
  
    
      Package: plaid

      Commit: 6b05c93dd17ced675529e8d2e1a61b225b6b644b

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:53:03 +0100

      Commit message:


	  
		 Fix p-value column descriptions in vignette

Corrected the description of the p-value columns in the vignette. 
    
  
    
      Package: plaid

      Commit: 2311c6034a58f53c2db6c57e1ee9648d1f1a7eac

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:46:46 +0100

      Commit message:


	  
		 Revise introduction for PLAID vignette

Updated the introduction to clarify the purpose and performance of PLAID. 
    
  
    
      Package: plaid

      Commit: e7345d4f9b3d764a49710162ec06e474bcc9eddb

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:30:40 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: 41312c2eb190ed3ddd3d2fb37de9dbfc41660134

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:28:54 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: ec92b027a66bba58ddc9f58c1e2d62c14cbde26e

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:26:15 +0100

      Commit message:


	  
		 Update DESCRIPTION 
    
  
    
      Package: plaid

      Commit: 3c168be94241c086b88ea6fa989314d3d2a6d5b2

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:12:06 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: 456907d2f031b8f6c4d9aec5a67b2c804b7aaa59

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:05:52 +0100

      Commit message:


	  
		 Merge branch 'main' of https://github.com/bigomics/plaid
 
    
  
    
      Package: plaid

      Commit: 2062c8d946fc9e4e7e84aeeac4254275f1f831c1

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:05:48 +0100

      Commit message:


	  
		 rename
 
    
  
    
      Package: plaid

      Commit: fbdeb9c113f1bbe2f3283380d8184335212dbce8

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:04:12 +0100

      Commit message:


	  
		 Update links in README for PLAID usage 
    
  
    
      Package: plaid

      Commit: a80c677a2ffab99e75d4817481bc737b96be226b

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:03:27 +0100

      Commit message:


	  
		 Update title of PLAID vignette 
    
  
    
      Package: plaid

      Commit: b20090ed470f74f68afa8270c35f75615688e04a

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:03:02 +0100

      Commit message:


	  
		 Update vignette title for clarity 
    
  
    
      Package: plaid

      Commit: 5c629854fe826de42e70aab4de04c27ff5b19586

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 14:00:20 +0100

      Commit message:


	  
		 Add Bootswatch default theme to pkgdown config 
    
  
    
      Package: plaid

      Commit: b1f06677b7d33a3c0f9bfcfb94422519d44cdc87

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:54:00 +0100

      Commit message:


	  
		 Update title and vignette index entry capitalization 
    
  
    
      Package: plaid

      Commit: 227a2162ce47d5b4223100f1884a4b8998bf460a

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:52:13 +0100

      Commit message:


	  
		 Update vignette index entry for PLAID 
    
  
    
      Package: plaid

      Commit: 12e06a9322cf03c2320077df12c0c7cfe99be5c9

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:50:22 +0100

      Commit message:


	  
		 Merge branch 'main' of https://github.com/bigomics/plaid
 
    
  
    
      Package: plaid

      Commit: dc025a70571d27e83095801d6ad861cdf0604e1a

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:50:14 +0100

      Commit message:


	  
		 rename files for ordering
 
    
  
    
      Package: plaid

      Commit: c7cc6b8b4ee700aa4d2862aaf73fa394d2feee59

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:42:12 +0100

      Commit message:


	  
		 Modify DESCRIPTION file for authors and dependencies

Updated authors' roles and R dependency version. 
    
  
    
      Package: plaid

      Commit: 20063a5a1d62a5030e936972f0b3a676e3875905

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:34:02 +0100

      Commit message:


	  
		 Merge branch 'main' of https://github.com/bigomics/plaid
 
    
  
    
      Package: plaid

      Commit: 52e606b6dcf3a8f6c75e70f1c0adc2dc0b2a03f6

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 13:33:56 +0100

      Commit message:


	  
		 add pkgdown
 
    
  
    
      Package: plaid

      Commit: 4ab10432d9d2bd0634c682ace4cbdd35cd232841

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 12:26:59 +0100

      Commit message:


	  
		 Update vignette links in README.md to point to live site 
    
  
    
      Package: plaid

      Commit: 7e70015b4b5c8e6a35308c00f5755203ad40f0d6

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 10:15:21 +0100

      Commit message:


	  
		 Merge branch 'main' of https://github.com/bigomics/plaid
 
    
  
    
      Package: plaid

      Commit: 8adf530a8ecc824414b21cc354d9451cc3e93d9c

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 10:15:15 +0100

      Commit message:


	  
		 add html doc
 
    
  
    
      Package: plaid

      Commit: fb48db6209a3fe44b1123cd6f99b666450058096

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 09:03:51 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: f961f414dcdfead560e8218f409c6a8eaa53f48b

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 09:00:57 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: 19ca889539e83aa8cb08a3f5592c097e473e2e84

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 08:34:39 +0100

      Commit message:


	  
		 Update references section in README.md

Removed citation for the movie 'Spaceballs' and adjusted related text. 
    
  
    
      Package: plaid

      Commit: 4c3314fe4a024b06a175f5c1fff2e0f418ff321d

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 08:32:32 +0100

      Commit message:


	  
		 remove file
 
    
  
    
      Package: plaid

      Commit: 349b8978fbe6e8b0f4dd155dd5e7683074a8e802

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-11 08:30:56 +0100

      Commit message:


	  
		 add tartan design
 
    
  
    
      Package: plaid

      Commit: d78e0da65fe30980ef13d79d1039f30f2f5339a0

      Author:  Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-10 11:07:47 +0100

      Commit message:


	  
		 Merge pull request #4 from bigomics/fix-lapply

fix lapply to  have same behaviour as sapply 
    
  
    
      Package: plaid

      Commit: 980b75214de7682c322c53c5f692e1feb2940210

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-10 11:07:25 +0100

      Commit message:


	  
		 fix: restore read.gmt tests and fix write.gmt vector handling
 
    
  
    
      Package: plaid

      Commit: b47de33f6e8e6b1318983cd8cc20dcb9730b2c60

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 04:45:22 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: 33d348c8fb9f470740a5e05801e060710dd235d5

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 03:28:53 +0100

      Commit message:


	  
		 Update plaid-vignette.Rmd 
    
  
    
      Package: plaid

      Commit: 2384fd29b0e1847457a10fbd9c29d68bdbd59899

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 03:21:48 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: 765139fc6b4577406f98d601880413db9c7cfd36

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 03:20:52 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: 366c87315c26ffca42da5ef8b2dd22ee5659027f

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 03:09:28 +0100

      Commit message:


	  
		 Encourage users to recommend and support PLAID

Added a section encouraging users to support the project. 
    
  
    
      Package: plaid

      Commit: bab0df9fcda798022fa31e3b6c1b74ccf484f4d3

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 02:54:30 +0100

      Commit message:


	  
		 fix lapply to  have same behaviour as sapply
 
    
  
    
      Package: plaid

      Commit: b76ff8795d7928347c41f9e0775c707b5f1c8fd2

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 02:28:23 +0100

      Commit message:


	  
		 Add citation for Omics Playground article 
    
  
    
      Package: plaid

      Commit: 3d62848beaff7436c262a9b370bfb11570b12bc9

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 02:18:16 +0100

      Commit message:


	  
		 add new designs
 
    
  
    
      Package: plaid

      Commit: c4fcb39143d7274d3a15c69406ac20b135891d77

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 01:50:43 +0100

      Commit message:


	  
		 Reorder warning message for clarity 
    
  
    
      Package: plaid

      Commit: 6d7cdbaec5f2be458ba7f6ec6d4710385b953c3b

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-10 01:45:16 +0100

      Commit message:


	  
		 Update references section in README.md

Added citation 
    
  
    
      Package: plaid

      Commit: 9487b124e51d7aa2015850122cf9f547ad4aae19

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-09 23:12:54 +0100

      Commit message:


	  
		 Reorder key features in README.md 
    
  
    
      Package: plaid

      Commit: 1b82e1bae2fbc699fe20e7f5734405cc80486439

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-09 23:11:59 +0100

      Commit message:


	  
		 Fix typo in README.md for PLAID description 
    
  
    
      Package: plaid

      Commit: 487f3a597389b0486bea409986dfcf5c3a8a6b22

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-09 23:06:43 +0100

      Commit message:


	  
		 Revise README for PLAID with logo

Updated the README adding logo and to improve clarity and add key features. 
    
  
    
      Package: plaid

      Commit: fdcee809f50a90b46866826f3069566cee78cf2f

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-09 22:20:05 +0100

      Commit message:


	  
		 add logo
 
    
  
    
      Package: plaid

      Commit: f4d8785211fa38973b1d66f991c9664605aec355

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-06 13:20:45 +0100

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: plaid

      Commit: a6ceafb6fb045571a4ea3dd6e92768e7bb09d5a8

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-06 13:17:59 +0100

      Commit message:


	  
		 Improve wording for gene set scoring explanation

Corrected phrasing for clarity and improved readability. 
    
  
    
      Package: plaid

      Commit: 47aba32cbf2d68c2d905f3be9e33aeba6f4967a6

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-06 13:16:59 +0100

      Commit message:


	  
		 Enhance README with PLAID features and performance

Added information about PLAID's simulation capabilities and efficiency compared to traditional algorithms. 
    
  
    
      Package: plaid

      Commit: 4b49b23133b4f968abb48b759caad1fcfa870c08

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 11:25:47 +0100

      Commit message:


	  
		 adress dontrun issue
 
    
  
    
      Package: plaid

      Commit: c17cd057ad7b383a7f0f6a335162bceedc566c91

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 11:07:05 +0100

      Commit message:


	  
		 Fix: Replace matG with G in fc_ttest function

The fc_ttest function was incorrectly referencing 'matG' instead of 'G'
when calling gset_averageCLR. The parameter name is 'G' in the function
signature, so it should use 'G' not 'matG'.

This bug was causing test failures in CI/CD environments.
 
    
  
    
      Package: plaid

      Commit: 2b574b32aeb80e80daa0d7112a001b0be0285669

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 11:02:07 +0100

      Commit message:


	  
		 test bioc-utils.R
 
    
  
    
      Package: plaid

      Commit: 0e86a40d57df30d02de8340bb22c9fe118d70ea1

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 10:59:08 +0100

      Commit message:


	  
		 test gmt-utils.R
 
    
  
    
      Package: plaid

      Commit: 2e4621cbdbfdbe2bb18d0f20044097d15db35955

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 10:49:23 +0100

      Commit message:


	  
		 test stats.R
 
    
  
    
      Package: plaid

      Commit: 529504db90a9d59b0dbea615c38582b3e1c57364

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 10:33:34 +0100

      Commit message:


	  
		 test plaid.R
 
    
  
    
      Package: plaid

      Commit: 9a3439c2ff8310509fd21e98f81882bc4808f20c

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-06 10:27:57 +0100

      Commit message:


	  
		 Merge branch 'main' of https://github.com/bigomics/plaid
 
    
  
    
      Package: plaid

      Commit: 70421349810ca018420a708dd24daeb7de9ef440

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-06 09:52:47 +0100

      Commit message:


	  
		 Revise README title and add references

Updated project title and added references section. 
    
  
    
      Package: plaid

      Commit: 3fc28bc19db3c5e66394d5f7ba4edd556c1ef19a

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 17:05:19 +0100

      Commit message:


	  
		 initial news file
 
    
  
    
      Package: plaid

      Commit: 80a8bf9c329af62d8b54877175bea3901bd7de9e

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 17:03:11 +0100

      Commit message:


	  
		 move makefile/env file to inst/
 
    
  
    
      Package: plaid

      Commit: a37660a1edb4ad3e272c1ba07c16588516cc71ef

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 17:00:57 +0100

      Commit message:


	  
		 sapply -> vapply
 
    
  
    
      Package: plaid

      Commit: 8c361451c5d73bd955997c7c9a206104fc01ae1a

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 16:58:34 +0100

      Commit message:


	  
		 use seq_ instead of 1:n
 
    
  
    
      Package: plaid

      Commit: 9cf31f69bbf9188c4b8d4211ca8a61a7c0d756af

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 15:44:28 +0100

      Commit message:


	  
		 simplify readme
 
    
  
    
      Package: plaid

      Commit: da5588f955ee7feb5bc7724ea6cfdbb6562af5ae

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 11:55:58 +0100

      Commit message:


	  
		 add codecov badge
 
    
  
    
      Package: plaid

      Commit: 31d7d1df3c1a29282663734cc9e2949bf2c12727

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-10-30 11:49:08 +0100

      Commit message:


	  
		 inject codecov token
 
    
  
    
      Package: SpliceImpactR

      Commit: 72ddfcfc3d107599af3f2c281eb8f955eb582577

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2025-11-12 10:23:14 -0500

      Commit message:


	  
		 Merge branch 'main' into devel
 
    
  
    
      Package: SpliceImpactR

      Commit: a4161eaa78f91a39e040774c68e38c0be00212a4

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2025-11-12 10:22:31 -0500

      Commit message:


	  
		 NEWS for 0.99.2
 
    
  
    
      Package: SpliceImpactR

      Commit: 360f99246394bb828b235839b09cec9f38509d1c

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2025-11-12 10:12:04 -0500

      Commit message:


	  
		 bump version & re-roxygenize
 
    
  
    
      Package: SpliceImpactR

      Commit: 7c5d623c9959d6c44ab17f93cdcf32b9a9084d0d

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2025-11-12 10:11:52 -0500

      Commit message:


	  
		 hotfix: replace |> with %>%
 
    
  
    
      Package: goatea

      Commit: fb910cec5441e6a6cce28c731938ac3b8054035e

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-11-12 16:10:18 +0100

      Commit message:


	  
		 Local install EnhancedVolcano to Biocccheck build and install for devel
 
    
  
    
      Package: CalibraCurve

      Commit: 6ea93aae3dc8fb10eee76b7ee4a996d7f64398f8

      Author:  Karin Schork <schorkka@mpc-domain.local> 

      Date: 2025-11-12 15:40:04 +0100

      Commit message:


	  
		 fix bug for all-in-one plots where plot was not saved
 
    
  
    
      Package: goatea

      Commit: 32901e83e83f0067b4ff35238e666b7660849bb9

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-11-12 15:07:54 +0100

      Commit message:


	  
		 Wrapped EnhandcedVolcano call with install message, as package is not building well currently, added to Suggests
 
    
  
    
      Package: GSVA

      Commit: 13f832d105c9a52b7bc26f05176254876a59f4d8

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-12 14:34:40 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: GSVA

      Commit: 60aae671bee4cda9abd5209468cd033f75595815

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-12 14:34:27 +0100

      Commit message:


	  
		 Updated documentation and simplified regression tests
 
    
  
    
      Package: goatea

      Commit: 68621d03170d30c846121665648faff923b03d7c

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-11-12 14:24:15 +0100

      Commit message:


	  
		 Merge resolve version
 
    
  
    
      Package: goatea

      Commit: 015456423e3cc69180b915c920db8e4f023d8bdd

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-11-12 14:17:29 +0100

      Commit message:


	  
		 Updated plots, docs, and fixed vignette loading for Bioconductor
 
    
  
    
      Package: goatea

      Commit: d1aee2557d59e1fce86ddec96944eff005d1b3ac

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-10-29 15:15:19 +0100

      Commit message:


	  
		 Updated and fixed linking to .css coloring
 
    
  
    
      Package: goatea

      Commit: 5d35f1ba162024a1f62cde0798b468b8aafab545

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-10-29 15:14:49 +0100

      Commit message:


	  
		 Updated plot format
 
    
  
    
      Package: goatea

      Commit: 12eaa8126d964c8f0bdf85c9fd8c1f65badb4b82

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-10-29 15:14:16 +0100

      Commit message:


	  
		 Updated colors
 
    
  
    
      Package: goatea

      Commit: 50a5a2e30d9731440e23d23e0ac172b0b456b9c2

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-10-29 15:13:53 +0100

      Commit message:


	  
		 Added pkgdown to README
 
    
  
    
      Package: goatea

      Commit: 19bfbca57a5af8ec723c0ff8fa5a352b2961128d

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2025-10-29 15:13:37 +0100

      Commit message:


	  
		 Fixed vignette, added docs/ and pkgdown/ site documentation
 
    
  
    
      Package: goatea

      Commit: 314d3e7db8d513ab775db9819b1b4bea8b9934e0

      Author:  Mauws <47570265+mauritsunkel@users.noreply.github.com> 

      Date: 2025-09-22 14:37:44 +0200

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: MetaProViz

      Commit: b92d5c0223421cdcbbbb7b61947eac5a2cfe481d

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2025-11-12 13:21:28 +0100

      Commit message:


	  
		 nothing
 
    
  
    
      Package: mCSEA

      Commit: 191deb9158d1f32997151f06eca3f1e26c3f91a1

      Author:  jordimartorell <jmartorellm@gmail.com> 

      Date: 2025-11-12 09:57:24 +0100

      Commit message:


	  
		 Add EPICv2 support
 
    
  
    
      Package: DMRcaller

      Commit: 67d400011292f5e834260d477c67ee2821935644

      Author:  nrzabet <r.zabet@qmul.ac.uk> 

      Date: 2025-11-12 08:39:45 +0000

      Commit message:


	  
		 fixed bug in filterVMRsONT.R
 
    
  
    
      Package: SpliceImpactR

      Commit: c4375abdd8bd36312d9aea91ea6995ecd06225de

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2025-11-11 22:09:37 -0500

      Commit message:


	  
		 Merge branch 'main' into bioc-devel-from-main
 
    
  
    
      Package: SpliceImpactR

      Commit: e7e10b4d6ccbebdb94dd6aa2029638a8301c7632

      Author:  Zachary Wakefield <zachpwakefield@gmail.com> 

      Date: 2025-11-11 22:05:49 -0500

      Commit message:


	  
		 NEWS for 0.99.1; ignore .DS_Store
 
    
  
    
      Package: SpliceImpactR

      Commit: 08ff740d4e94d5f3ffb338fb9f64418e2225277c

      Author:  Zachary Wakefield <zacharywakefield@Zacharys-MacBook-Pro-2.local> 

      Date: 2025-11-11 21:52:17 -0500

      Commit message:


	  
		 Bump to 0.99.1
 
    
  
    
      Package: SpliceImpactR

      Commit: a9d59a0b33b86dc7fef4bdcf8d46987875232aa2

      Author:  Zachary Wakefield <zacharywakefield@Zacharys-MacBook-Pro-2.local> 

      Date: 2025-11-11 21:52:17 -0500

      Commit message:


	  
		 Bump to 0.99.1
 
    
  
    
      Package: SpliceImpactR

      Commit: 2bd2ee1b1db14243473f42cb02d5e31c7bbd590b

      Author:  Zachary Wakefield <zacharywakefield@Zacharys-MacBook-Pro-2.local> 

      Date: 2025-11-11 21:47:19 -0500

      Commit message:


	  
		 Link upstream/devel (keep our tree)
 
    
  
    
      Package: SpliceImpactR

      Commit: f0b874cd134ae5516ed11bd2cf8f7f30052ab845

      Author:  Zachary Wakefield <zacharywakefield@Zacharys-MacBook-Pro-2.local> 

      Date: 2025-11-11 21:01:41 -0500

      Commit message:


	  
		 Merge upstream/devel into ours (keep our tree)
 
    
  
    
      Package: SpliceImpactR

      Commit: aa9baae2063785209c80cc2d6c7f8322f76eeb29

      Author:  Zachary Wakefield <zacharywakefield@Zacharys-MacBook-Pro-2.local> 

      Date: 2025-11-11 13:26:47 -0500

      Commit message:


	  
		 Initial clean commit of SpliceImpactR package
 
    
  
    
      Package: ChIPpeakAnno

      Commit: a293c4f1b41269208ce7e8d9ff5750ef5cf330e4

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-11-11 20:01:42 -0500

      Commit message:


	  
		 fix a typo
 
    
  
    
      Package: ChIPpeakAnno

      Commit: abd957f4b669120a52b972ff26c1b82d694b742f

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-11-11 20:01:07 -0500

      Commit message:


	  
		 Remove microRNAs
 
    
  
    
      Package: DESeq2

      Commit: 55c5b1fe161e6bcbf1bd3b2d852800d064c034c9

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-11 19:30:14 -0500

      Commit message:


	  
		 version bump
 
    
  
    
      Package: DESeq2

      Commit: 790929224bf2287892b5004a5f457ca92177653b

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-11 19:29:52 -0500

      Commit message:


	  
		 fix plotPCA for new ggplot2
 
    
  
    
      Package: crisprDesign

      Commit: 641310fc602f26ba6e0c1effc6fbc820c00c4d7d

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-11 15:28:25 -0800

      Commit message:


	  
		 Bumped version
 
    
  
    
      Package: TCGAutils

      Commit: c19b260f6d63bf6e86550368fd6f975a889590af

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-11 17:30:56 -0500

      Commit message:


	  
		 version bump 1.31.3
 
    
  
    
      Package: TCGAutils

      Commit: 140490ce4d972fbf2dfa45c8a5903ac787dd5bd8

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-11 09:54:00 -0500

      Commit message:


	  
		 use utils::tail
 
    
  
    
      Package: TCGAutils

      Commit: 87e31a650ba1809d64ec149b19421b0104fd1fd6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-11 09:49:47 -0500

      Commit message:


	  
		 use assay instead of x[[i]]
 
    
  
    
      Package: TCGAutils

      Commit: f086dcebbcb49b1784df6cc21231fa67ca100ff9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-11 09:49:30 -0500

      Commit message:


	  
		 simplify and use rowidx for mcols col
 
    
  
    
      Package: TCGAutils

      Commit: c211a012dfd41e7fd8bec61bf8fdddde0451aa29

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-11 09:42:49 -0500

      Commit message:


	  
		 separate .makeMiRNAListRanges from .makeListRanges
 
    
  
    
      Package: TCGAutils

      Commit: 5a8dc77ddb9883ca78556f7f4e6231edc44ca289

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-11 09:40:41 -0500

      Commit message:


	  
		 match tolower for rowIdx
 
    
  
    
      Package: TCGAutils

      Commit: 742bfb36d18a1019bd4eed263d3ebf8fee833138

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 15:21:32 -0500

      Commit message:


	  
		 use default "hg19" for .get_hsa_gff3
 
    
  
    
      Package: TCGAutils

      Commit: 53d5c13e2aaede31a27fc76cdd0ab81fb8ffb9d5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 15:21:12 -0500

      Commit message:


	  
		 fix .getRangesOfMir check
 
    
  
    
      Package: TCGAutils

      Commit: 4c037bd942533736e987a8f4ffe7a3915e199528

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-05 17:57:42 -0500

      Commit message:


	  
		 check for Bioc.gff installation in mirToRanges
 
    
  
    
      Package: TCGAutils

      Commit: 502b76ca7f18cdece265d745dbc2662b22cdbcf7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-05 17:53:55 -0500

      Commit message:


	  
		 update authors in simplifyTCGA
 
    
  
    
      Package: TCGAutils

      Commit: 8df0b1d33dd7cd9de24fe7439b212ed8d35de35f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-05 17:53:36 -0500

      Commit message:


	  
		 use miRNAmeConverter to translate and map miRNA IDs
 
    
  
    
      Package: TCGAutils

      Commit: 7c7be7dc424d9f8c96d8e7fb08221f6e4044c78b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-05 17:36:42 -0500

      Commit message:


	  
		 create helper to identify viable assays
 
    
  
    
      Package: TCGAutils

      Commit: c094feb1d821ac768a55adacb17e9585bdf3b817

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-06 16:55:05 -0500

      Commit message:


	  
		 restore use of mirToRanges
 
    
  
    
      Package: msa

      Commit: 5fe136a38165f0167db48b84c89a78533e94b97f

      Author:  UBod <ulrich@bodenhofer.com> 

      Date: 2025-11-11 21:00:51 +0100

      Commit message:


	  
		 fix of seq names for alignments created directly from files; version number bumped to 1.43.1
 
    
  
    
      Package: amplican

      Commit: dd29ebe32d71a8c5acd3461436a643d3f2ef7bd0

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2025-11-11 16:24:22 +0100

      Commit message:


	  
		 version is 1.33.1
 
    
  
    
      Package: amplican

      Commit: 2c637750471c8a9c9d8b96540b5e4e7b727b00ca

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2025-11-11 16:10:45 +0100

      Commit message:


	  
		 fix waffle and fix checks
 
    
  
    
      Package: crisprDesign

      Commit: b10fa102341adbd8fec90b086c713cfee25d40b1

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-10 16:34:12 -0800

      Commit message:


	  
		 Expanding on amino acids for missense_multiple variants
 
    
  
    
      Package: assorthead

      Commit: df6d34b7575fc917ef638acc370e9e9fc0ef5679

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-11-11 09:41:40 +1100

      Commit message:


	  
		 Updated versions for vendored Eigen and its downstreams.
 
    
  
    
      Package: scrapper

      Commit: 5daae9cf6743103045fe2925e3d79b723727e89c

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-11-11 09:51:44 +1100

      Commit message:


	  
		 Bumped version to rebuild with latest Eigen/irlba.
 
    
  
    
      Package: singIST

      Commit: 5b919d3f7b972ce44a99181dc8f22efb1047571a

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 22:14:25 +0100

      Commit message:


	  
		 solve timeout testthat
 
    
  
    
      Package: singIST

      Commit: 014f9f71b9b3075ed809f2d36c10739dc4a71e32

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 21:37:29 +0100

      Commit message:


	  
		 build
 
    
  
    
      Package: singIST

      Commit: 5a8d44df5f7925c0961f566a8359d89c5627958c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 20:55:58 +0100

      Commit message:


	  
		 Solve ERROR
 
    
  
    
      Package: singIST

      Commit: e0eab78634e4398b77dd8585696224bb5feb0723

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 20:53:09 +0100

      Commit message:


	  
		 Solve ERRORS
 
    
  
    
      Package: rhdf5

      Commit: d13ca6d8f263b17dbf323ba9f626d4e90b73fecc

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 11:48:55 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: rhdf5

      Commit: 110c2a8e5d516ab0ed35483c7ce20ac06e4b8148

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 11:48:37 +0100

      Commit message:


	  
		 Mention rchk fixes in NEWS
 
    
  
    
      Package: rhdf5

      Commit: dd7d6b187ff749dfebf1b879bebf9a7db4c8df9b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 11:28:35 +0100

      Commit message:


	  
		 Move SEXP in switch
 
    
  
    
      Package: rhdf5

      Commit: 010742f202f13b8bb5028406abc20fd95a8871c8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-10 10:47:00 +0100

      Commit message:


	  
		 Use PROTECT() on R_getClassDef()
 
    
  
    
      Package: rhdf5

      Commit: 1a58c69bfe0fa524024e3733358b9a945aaa3b0f

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-09 22:30:46 +0100

      Commit message:


	  
		 Use PROTECT() on mkString()
 
    
  
    
      Package: rhdf5

      Commit: 131f0a026764f2d3f375fe2fe554b608ab50d0dd

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 15:44:54 +0200

      Commit message:


	  
		 Balance PROTECT() and UNPROTECT() calls

within a given function
 
    
  
    
      Package: rhdf5

      Commit: c7a9427ecc3cd1f1562b58f93ab2b6c77c76b636

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 15:41:43 +0200

      Commit message:


	  
		 Move UNPROTECT() after warning()
 
    
  
    
      Package: rhdf5

      Commit: ca369278f07af6e17b0f25c5a1da83bc687ab2a2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-09 21:09:16 +0100

      Commit message:


	  
		 Rbuildignore git-blame-ignore-rev
 
    
  
    
      Package: rhdf5

      Commit: 1539dafc73f14c9d5e5591512ac3350a817928f5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-09 19:27:21 +0100

      Commit message:


	  
		 Remove markdown syntax from NEWS
 
    
  
    
      Package: rhdf5

      Commit: bf702fce8cd6672092c6d09e5b1b33ee487e4a24

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-09 14:37:52 +0100

      Commit message:


	  
		 Add missing closing brace in NEWS
 
    
  
    
      Package: terraTCGAdata

      Commit: 0a9bb0587a8eba876cd550f490cce9306116606c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 14:12:00 -0500

      Commit message:


	  
		 version bump 1.15.1
 
    
  
    
      Package: terraTCGAdata

      Commit: 006c2e4141e658e1ebbe9518a9c49adcfda6f0ce

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 14:11:55 -0500

      Commit message:


	  
		 bump RoxygenNote version
 
    
  
    
      Package: terraTCGAdata

      Commit: c08d5692eb020de6c9945a9c28b10c742caf835f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 14:11:46 -0500

      Commit message:


	  
		 replace AnVILGCP::gcloud_exists with GCPtools::gcloud_exists
 
    
  
    
      Package: TCGAutils

      Commit: a514bf5f6a21cb961c87ecfa75925bf147e46cbb

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 14:08:35 -0500

      Commit message:


	  
		 version bump 1.31.2
 
    
  
    
      Package: TCGAutils

      Commit: ed585c5553f356f2eacc234d630a07581a4484eb

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 14:08:31 -0500

      Commit message:


	  
		 update makeGRangesListFromCopyNumber example
 
    
  
    
      Package: methodical

      Commit: a177cc248e3ccb600ee287838fa65c0d16072241

      Author:  Richard Heery <richardheery@gmail.com> 

      Date: 2025-11-10 17:53:44 +0000

      Commit message:


	  
		 Added make meth RSE files
 
    
  
    
      Package: AnVILGCP

      Commit: 3081ee6f8737ad9d537ae459cad0c4b083049939

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 12:46:55 -0500

      Commit message:


	  
		 version bump 1.5.2
 
    
  
    
      Package: AnVILGCP

      Commit: 264ea1e7fdbe96ddd2f3636a88afb9f6f0017f59

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 12:46:50 -0500

      Commit message:


	  
		 use GCPtools::gcloud_exists
 
    
  
    
      Package: singIST

      Commit: d85edec87cd43493d83b70c9917dc01c1004b194

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 18:39:31 +0100

      Commit message:


	  
		 SOLVE errors
 
    
  
    
      Package: singIST

      Commit: bfb61e1ee5d24eb4167825137b27e6560feb10b2

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 18:35:38 +0100

      Commit message:


	  
		 Solve ERRORS
 
    
  
    
      Package: AnVILBase

      Commit: fb8f17528d0accffce084d84ebd96826f4f5fb10

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 12:20:41 -0500

      Commit message:


	  
		 version bump 1.5.1
 
    
  
    
      Package: AnVILBase

      Commit: ba47e136b1513f5e93aa1f8369f299bb6d46e25f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 12:20:36 -0500

      Commit message:


	  
		 version bump RoxygenNote
 
    
  
    
      Package: AnVILBase

      Commit: 53ac8c174dceca8a2b371a8ba3c903b0b495385b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-10 12:20:27 -0500

      Commit message:


	  
		 use GCPtools::gcloud_exists
 
    
  
    
      Package: singIST

      Commit: 778a6086a0b03f5e659f53e7a9d985dd13d17938

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 17:21:09 +0100

      Commit message:


	  
		 Solve TIMEOUT tests
 
    
  
    
      Package: ChIPpeakAnno

      Commit: 04edcb5144fd8f01d3bfd82f24c3d1b41422a3a6

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-11-10 10:43:29 -0500

      Commit message:


	  
		 remove microRNAs
 
    
  
    
      Package: singIST

      Commit: 36324619e3dee00e86fa2de83278212b83c7f76c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 16:35:45 +0100

      Commit message:


	  
		 Solve TIMEOUT reduce time of examples
 
    
  
    
      Package: Pirat

      Commit: cb2c330e9e1dc85b5bf146cfe4529d62e12350f9

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-10 15:59:09 +0100

      Commit message:


	  
		 Adapt pytorch version to OS
 
    
  
    
      Package: singIST

      Commit: 9af2a6d04022c659daef600fd59d79572463ef9d

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-11-10 11:51:52 +0100

      Commit message:


	  
		 Bump version, fix build ERROR
 
    
  
    
      Package: singIST

      Commit: fffdd61b4d4ef732758ed429d727710beda85824

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 20:36:04 -0400

      Commit message:


	  
		 Remove object@counts error
 
    
  
    
      Package: singIST

      Commit: 76a497163d5dde1aeb8e8a642a3b7379deacf5ca

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 16:13:00 -0400

      Commit message:


	  
		 WP to WIKIPATHWAYS
 
    
  
    
      Package: singIST

      Commit: 69682a4f44f21307056eba00ec5acc8e3da53252

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 16:07:15 -0400

      Commit message:


	  
		 Wikipathways to WP
 
    
  
    
      Package: singIST

      Commit: f37b3ef3720c46290b6c0acdbe7fca2174213a9f

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 15:21:15 -0400

      Commit message:


	  
		 Restrict character "_" in mapping.organism target and base classes. This character is a special one restricted to Seurat.
 
    
  
    
      Package: singIST

      Commit: 7d59977a4d36b6d415370a11c3a22298a520dd4a

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 15:15:24 -0400

      Commit message:


	  
		 Remove debugging prints
 
    
  
    
      Package: singIST

      Commit: eaa45ff06a5cf425bfb4a3ac14d6847c867afd47

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 14:55:48 -0400

      Commit message:


	  
		 Remove debugging
 
    
  
    
      Package: singIST

      Commit: 971afcf743f74c2d22d9c89f59d8a8e96771fd58

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 14:55:38 -0400

      Commit message:


	  
		 Add check for non-negative Seurat counts layer
 
    
  
    
      Package: singIST

      Commit: e88226d168d8cd7cc3c47cebb2d75d1c80c6ab9a

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 14:22:10 -0400

      Commit message:


	  
		 debugging
 
    
  
    
      Package: singIST

      Commit: 972131c896ba393f34dd8f2e12efb5fa7604fd84

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-24 14:07:41 -0400

      Commit message:


	  
		 debug
 
    
  
    
      Package: singIST

      Commit: fa3774ca4d7e0b635ca0bcdea195ef63af086250

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-23 20:54:23 -0400

      Commit message:


	  
		 update findmarkers
 
    
  
    
      Package: singIST

      Commit: 7829e6a0723a5f4d1b134a2dcee36b38f93ab2ee

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-23 20:53:33 -0400

      Commit message:


	  
		 update libraries
 
    
  
    
      Package: singIST

      Commit: 91e73abccbd6163a1cec6f9d801fa9834f30e1bf

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-23 20:52:23 -0400

      Commit message:


	  
		 Include pseudobulk and update FindMarkers and findMarkers for sce objects
 
    
  
    
      Package: singIST

      Commit: 26ce4b7f204b0e98269662778d486cc61552920b

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 21:52:43 -0400

      Commit message:


	  
		 ttest
 
    
  
    
      Package: singIST

      Commit: 4b2f8a7329d5c52b816e093cc413a38c4e90fe6c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 21:37:00 -0400

      Commit message:


	  
		 wilcox limma
 
    
  
    
      Package: singIST

      Commit: ec41f77e2c3e6b97c3a3e54762d59f675f47407a

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 21:14:46 -0400

      Commit message:


	  
		 wilcox log2fc but with pseudobulk
 
    
  
    
      Package: singIST

      Commit: 95d032d8bd0ae1c7d95a6de251024dd003733a0e

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 20:49:23 -0400

      Commit message:


	  
		 na.rm TRUE
 
    
  
    
      Package: singIST

      Commit: def6c95cfa8abac0a3a2cd267e02c8ae63b2e3eb

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 18:24:27 -0400

      Commit message:


	  
		 debugging
 
    
  
    
      Package: singIST

      Commit: 584fb40aacd277984a82e5bad6f3dea721cb9339

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 15:38:12 -0400

      Commit message:


	  
		 round for ambient RNA
 
    
  
    
      Package: singIST

      Commit: c11251a1994d254d709030249e0f748258255613

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 15:13:06 -0400

      Commit message:


	  
		 slot counts aggregate in expression
 
    
  
    
      Package: singIST

      Commit: 8571686b476ad4d4260642085afef136f66b95ec

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 14:55:27 -0400

      Commit message:


	  
		 debugging
 
    
  
    
      Package: singIST

      Commit: babca2359102ee66236e21193cffa9c3993d44f9

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 14:37:36 -0400

      Commit message:


	  
		 Remove slot
 
    
  
    
      Package: singIST

      Commit: 7281985addaf562bcbd1eb5299d25c4b3f73cf60

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 14:19:00 -0400

      Commit message:


	  
		 slot counts
 
    
  
    
      Package: singIST

      Commit: b632e0b01e73af98f472d967b25b2d0dec22df59

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 14:09:31 -0400

      Commit message:


	  
		 Use DESeq2
 
    
  
    
      Package: singIST

      Commit: 42e317bb86b9085c5ab49ec51ee58fbe4d1e4f47

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 14:00:09 -0400

      Commit message:


	  
		 solve
 
    
  
    
      Package: singIST

      Commit: 224dbdad8bc971291ca0a4354f47ae960daadec0

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 13:39:58 -0400

      Commit message:


	  
		 solve
 
    
  
    
      Package: singIST

      Commit: 100ebdd7dfc241f71a4b18766a3cef01ad4acd26

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 12:52:00 -0400

      Commit message:


	  
		 log2FC via DESeq2 pseudobulk
 
    
  
    
      Package: singIST

      Commit: 977946be04e7234450328ae55f864e3d153e3dbf

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-21 12:39:40 -0400

      Commit message:


	  
		 Compute log2FC of disease model with pseudobulk and DESeq2 via FindMarkers
 
    
  
    
      Package: singIST

      Commit: d4f3e91fcceadacaf1bf03c1c96e54a9e7505d5b

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-20 11:10:23 -0400

      Commit message:


	  
		 Translate to log2FC
 
    
  
    
      Package: singIST

      Commit: 15f4352b4baa8c6ba55798ac75c17356c93e1693

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-15 08:58:55 -0400

      Commit message:


	  
		 Solve symmetry
 
    
  
    
      Package: singIST

      Commit: 3deb8c30d59d1650971844647d53e55540a04135

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-15 08:51:43 -0400

      Commit message:


	  
		 Test transformation change log2FC
 
    
  
    
      Package: singIST

      Commit: 6948aa5d1bd6bd52cfe9dae411f11d1fa011c71e

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-14 16:19:20 -0400

      Commit message:


	  
		 Make FC effect symmetric for positive and negative log2FC
 
    
  
    
      Package: singIST

      Commit: fc8710fc23b5861e2ceddbf263dce1101d3c36c7

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-11 18:53:51 -0400

      Commit message:


	  
		 Solve ordering error in MatrixToBlock function
 
    
  
    
      Package: singIST

      Commit: 84bd510c6a672ee4e4bb2215d592a537a681d8d0

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-11 17:23:05 -0400

      Commit message:


	  
		 Update test to account removal of features
 
    
  
    
      Package: singIST

      Commit: f5b601bdddc8b0ae2052bec4fa0eef163655bb31

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-11 17:21:28 -0400

      Commit message:


	  
		 Correct \sum
 
    
  
    
      Package: singIST

      Commit: eb1dc7aeb39cec186617672c86e8c18e5a6f3b59

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-11 10:46:21 -0400

      Commit message:


	  
		 Amend typo
 
    
  
    
      Package: singIST

      Commit: 1b04c0f347339de9eefeaedde50f2ed66579fc74

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-11 10:40:06 -0400

      Commit message:


	  
		 Amend error
 
    
  
    
      Package: singIST

      Commit: 3f233afe37e75d55a32f04a47de9fa462f27f695

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-11 10:31:03 -0400

      Commit message:


	  
		 Only impute at each fold not every quantile per fold
 
    
  
    
      Package: singIST

      Commit: 959ac9c564f782b4388c1966c568705ba7e39474

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-10 21:15:56 -0400

      Commit message:


	  
		 Solve X.dim problem
 
    
  
    
      Package: singIST

      Commit: 3b818effa24618d0042e2ee59b6b2d31c095c295

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-10 16:14:34 -0400

      Commit message:


	  
		 Update documentation to include KCV
 
    
  
    
      Package: singIST

      Commit: dce73a3de015130c6232a0a65c8d870190e4ada4

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-10 16:13:55 -0400

      Commit message:


	  
		 Include imputation step within K-CV step via imputeMFA and MFA projection onto validation set
 
    
  
    
      Package: singIST

      Commit: 4fa2e7fd141b98b7e2f58feafb96b300061ed0ab

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-08 21:05:31 -0400

      Commit message:


	  
		 Include F1 set to 0 in original function
 
    
  
    
      Package: singIST

      Commit: 0808d68bbb57b69bc32467f885db04d1e2fcc928

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-08 19:33:48 -0400

      Commit message:


	  
		 Correct derivation of null distribution by generating new fold combination
 
    
  
    
      Package: singIST

      Commit: 7055c72af8b199d868d2b4218927f83a7389c87c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-08 15:29:50 -0400

      Commit message:


	  
		 Allow missing values
 
    
  
    
      Package: singIST

      Commit: 47d558f843d8d20bc5407fc49933d571b094197c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-08 14:14:03 -0400

      Commit message:


	  
		 Include automated imputation in CV
 
    
  
    
      Package: singIST

      Commit: ed9df01539a289e3402096f03a68fbd95c756609

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-07 22:11:40 -0400

      Commit message:


	  
		 length
 
    
  
    
      Package: singIST

      Commit: faabb0e0de661f2e82f75879501420998aac5cf3

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-07 22:05:45 -0400

      Commit message:


	  
		 amend non possible permutations
 
    
  
    
      Package: singIST

      Commit: 23b2ea62cd32451df6de2185c2dcd4cf102e3fbf

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-07 18:34:10 -0400

      Commit message:


	  
		 amend arguments
 
    
  
    
      Package: singIST

      Commit: 069ec68aa1d4a492c5869f484481d5f8e54d045c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-07 18:14:56 -0400

      Commit message:


	  
		 new features
 
    
  
    
      Package: singIST

      Commit: fcfd1b4b77e8e6b51e02471285e19fbed1216b13

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-07 17:25:11 -0400

      Commit message:


	  
		 Add new features
 
    
  
    
      Package: singIST

      Commit: d5ef953d84472935c350f3ef8497382c267b3c3c

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-06 15:04:24 -0400

      Commit message:


	  
		 Add a KCV with repetitions functions self-made as asmbPLS is not reproducible for this CV
 
    
  
    
      Package: singIST

      Commit: 7c954b4a6db10cfc5472569140974d599bd86ba5

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-05 10:14:31 -0400

      Commit message:


	  
		 Amend error indexing
 
    
  
    
      Package: singIST

      Commit: 84e66518ee049ac1aa2a8b393eb5efd13e4b34e6

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-05 08:41:36 -0400

      Commit message:


	  
		 Include variable ncv
 
    
  
    
      Package: singIST

      Commit: 3bddebe94c9954984f5fb90b7e591315354b9ecd

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2025-07-04 19:28:41 -0400

      Commit message:


	  
		 Allow pseudobulk matrix to have more celltypes than analyzed
 
    
  
    
      Package: Pirat

      Commit: b2fe8bb6469c8072b647d376d35dadf14ac30db0

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-10 12:12:07 +0100

      Commit message:


	  
		 Add +cpu
 
    
  
    
      Package: MetaProViz

      Commit: 3e11bbba1ad8ed64a791892bc97437eff7dbcb01

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-07 12:56:07 +0100

      Commit message:


	  
		 Bump version: 3.99.21 → 3.99.22
 
    
  
    
      Package: MetaProViz

      Commit: d1382ad1b6b9348cccb10f547461e500e982b01f

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-07 12:56:02 +0100

      Commit message:


	  
		 docs rebuild
 
    
  
    
      Package: MetaProViz

      Commit: 131b42f5932275fd08be88f0b5bb21908d9870db

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-07 12:55:47 +0100

      Commit message:


	  
		 long lines in docstring examples
 
    
  
    
      Package: damidBind

      Commit: 14520eee442d915269b15403587f53424dcb6446

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 03:07:28 +0000

      Commit message:


	  
		 Updated to 0.99.4
 
    
  
    
      Package: damidBind

      Commit: 924f592f74b39438ef3e2a78b4e95c98fe61f2e9

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:59:33 +0000

      Commit message:


	  
		 Updated vignette with details on FDR usage, gene expression differences, and accessor methods.
 
    
  
    
      Package: damidBind

      Commit: f7080a2f15f503aabc2b85308469cf5acb9860fc

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:59:02 +0000

      Commit message:


	  
		 Updated unit tests
 
    
  
    
      Package: damidBind

      Commit: 1090b594f08371ed26474b54ea54534452772083

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:58:02 +0000

      Commit message:


	  
		 Updated documentation
 
    
  
    
      Package: damidBind

      Commit: 9a6caf72248232a05c44d30f9db46cb8f45c4265

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:56:48 +0000

      Commit message:


	  
		 Added in FDR filtering functions
 
    
  
    
      Package: damidBind

      Commit: a85b9508af95047995d89b19b2647ac1392db55c

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:56:33 +0000

      Commit message:


	  
		 Minor documentation fixes
 
    
  
    
      Package: damidBind

      Commit: 7bfe786e42068605d3efb0875819e0e37acd409f

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:56:13 +0000

      Commit message:


	  
		 Adapted to allow for FDR columns
 
    
  
    
      Package: damidBind

      Commit: f6e4537965fccd597b77732b68d51f8adcf60d5e

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:55:44 +0000

      Commit message:


	  
		 Added in FDR filtering capabilities
 
    
  
    
      Package: damidBind

      Commit: b0001b72899615a6890737fc0f9ccdd6fa5c1ef6

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:55:23 +0000

      Commit message:


	  
		 Added in FDR filtering capabilities
 
    
  
    
      Package: damidBind

      Commit: 2fd41877e35e147e494c64a0f52d89c4f330bc64

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:54:58 +0000

      Commit message:


	  
		 Removed and consolidated with other methods
 
    
  
    
      Package: damidBind

      Commit: 43e551b62304317b5c61d1ed04adc56761422183

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:54:33 +0000

      Commit message:


	  
		 Minor grammar changes
 
    
  
    
      Package: damidBind

      Commit: 5fb5ade2282b5d634e16cfea71cb1b0d889f72b3

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:54:17 +0000

      Commit message:


	  
		 Split off acccessor methods to this file, added in `expressed` accessor.
 
    
  
    
      Package: damidBind

      Commit: d753cddecf8f5cfe97fc7cfb51f690a35ab5e26c

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:53:42 +0000

      Commit message:


	  
		 Adapted to use GRanges structure for binding data
 
    
  
    
      Package: damidBind

      Commit: b2834ba4c35e21f246d0e591dc982c9e1ec67e08

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:53:16 +0000

      Commit message:


	  
		 Minor internal fixes
 
    
  
    
      Package: damidBind

      Commit: 475f29311e88ef23f62491c08bb9ffde82ba92a8

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:52:33 +0000

      Commit message:


	  
		 Fixed roxygen documentation, added in expressed() method
 
    
  
    
      Package: damidBind

      Commit: e5fc2982f0f0bfdfa3438cf7608992a9380606de

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:52:03 +0000

      Commit message:


	  
		 Refactored and simplified, using GRanges internals
 
    
  
    
      Package: damidBind

      Commit: 8a955dae0bcc20ca613ba6db4ca3faecdb93200a

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:51:29 +0000

      Commit message:


	  
		 FDR model and calculation routines (optional for RNA Pol occupancy)
 
    
  
    
      Package: damidBind

      Commit: 38f905b9f5ad9ceca009ee9cbb74cb2b48a73fff

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:50:53 +0000

      Commit message:


	  
		 Updated to use GRanges internals
 
    
  
    
      Package: damidBind

      Commit: b81486322a945c98cf8f3c9f91f7e228270e36eb

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:50:19 +0000

      Commit message:


	  
		 Substantial refactor to provide greater clusterProfiler method compatibility and functionality downstream.
 
    
  
    
      Package: damidBind

      Commit: fcf81cbf671622ce20e1d6268a8aaabda0297e80

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-10 02:49:22 +0000

      Commit message:


	  
		 Updates for 0.99.4
 
    
  
    
      Package: damidBind

      Commit: 28f37c86f9f7c07cb366513dcb8b9fb6d7785e28

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 04:51:36 +0000

      Commit message:


	  
		 Updated documentation
 
    
  
    
      Package: damidBind

      Commit: 52b8fd5ebae08456cf60edf8b2dc7e0757504a5a

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 04:51:05 +0000

      Commit message:


	  
		 New plotting options: wrap_labels, fit_labels, abbrev_terms, abbrevs
 
    
  
    
      Package: damidBind

      Commit: 51483a96778ef8dda92fa7219f71b110a58ff9c7

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 04:50:28 +0000

      Commit message:


	  
		 Added more graphic params: label_fill, text_fill.  Fixed highlight point palette luminosity.
 
    
  
    
      Package: damidBind

      Commit: 8000f567225e820fcd354ddc88a57e046ad6d9d1

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 04:01:26 +0000

      Commit message:


	  
		 Additional configuration params (trackheight, peakCol, trackCol)
 
    
  
    
      Package: damidBind

      Commit: 41d9892607257b07a60206979e015a9275994369

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 04:00:49 +0000

      Commit message:


	  
		 Added wrap_labels and fit_labels plotting params
 
    
  
    
      Package: damidBind

      Commit: ff9b5bb7e47f025aee6341fca074e100788a4f4f

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 04:00:09 +0000

      Commit message:


	  
		 Minor tidying
 
    
  
    
      Package: damidBind

      Commit: 7ba969310ac24a09a1f9b9bb4cd7e0e29762e471

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 03:59:50 +0000

      Commit message:


	  
		 Updated NEWS
 
    
  
    
      Package: damidBind

      Commit: 9ecc53d5fce4c5bc264fe81415a9bb121ad1c7ee

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-11-06 03:59:37 +0000

      Commit message:


	  
		 Added imports
 
    
  
    
      Package: epiSeeker

      Commit: aae62bb08ae1f461eaee1aad0239a73ccb14a98e

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-10 09:20:45 +0800

      Commit message:


	  
		 update docs
 
    
  
    
      Package: epiSeeker

      Commit: f2afec9a604f1ccd3a124743440bb3847e5ed91b

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-09 22:34:18 +0800

      Commit message:


	  
		 Update for demo data and reduce dependency
 
    
  
    
      Package: epiSeeker

      Commit: ec5c62f787adf2eaf10c68945923962dc879e158

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-07 13:05:36 +0800

      Commit message:


	  
		 update docs
 
    
  
    
      Package: epiSeeker

      Commit: 4892c2d6352fd7f42f13fcdac7524639002a7c7a

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-07 12:37:01 +0800

      Commit message:


	  
		 add demo file for hg38
 
    
  
    
      Package: epiSeeker

      Commit: 4b85eb3d1595003dc825f3ebbaacc1c4d524feca

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-06 22:13:45 +0800

      Commit message:


	  
		 BiocCheck suggest Avoid the use of paste in condition signals
 
    
  
    
      Package: epiSeeker

      Commit: e1c9945a44c34d8efa5d81009adbd21a73c5bc1f

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-06 22:09:49 +0800

      Commit message:


	  
		 BiocCheck suggest replace cat with message
 
    
  
    
      Package: epiSeeker

      Commit: fcf445746e54fb0e84034465f8291b87cee77c6b

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-06 21:59:02 +0800

      Commit message:


	  
		 BiocCheck suggest replace tab
 
    
  
    
      Package: epiSeeker

      Commit: 497687458762839c42c29f60e21dc047d0238639

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-06 21:50:22 +0800

      Commit message:


	  
		 BiocCheck suggested remove suppressWarnings
 
    
  
    
      Package: epiSeeker

      Commit: b360c8490a05c20ccbea2a47697bcfbb84ba8e71

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-06 21:41:29 +0800

      Commit message:


	  
		 BiocCheck suggested biocViews: GeneRegulation
 
    
  
    
      Package: epiSeeker

      Commit: 1662152dc24209cf3a45f6d0a6cd1c15c69c75a4

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-06 21:31:38 +0800

      Commit message:


	  
		 BiocCheck note for sapply
 
    
  
    
      Package: GSVA

      Commit: 15ccfa33bdc4d1f54f66fdcb5fd498040f8da1cc

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-09 21:23:25 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: GSVA

      Commit: f6e2a15ed5a62a20b73980428327efb71bbef00d

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-09 21:23:11 +0100

      Commit message:


	  
		 Fix on the recovery from errors found during parallelization
 
    
  
    
      Package: sesameData

      Commit: a18b70936e2d6655f51bd837f79535a453d5e5d5

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-09 11:22:18 -0500

      Commit message:


	  
		 bump to 1.29.2
 
    
  
    
      Package: DESeq2

      Commit: d0d877d0394df39d1c9dd9ea02ae94b74ccf5a08

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-09 07:11:47 -0500

      Commit message:


	  
		 version bump, pushed to devel and release 3.22, fixes #121
 
    
  
    
      Package: DESeq2

      Commit: 366d1170af104aba655be6eee4b6e087dfb5cb1c

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-11-09 07:10:05 -0500

      Commit message:


	  
		 fix broken vignette link
 
    
  
    
      Package: ngsReports

      Commit: aec27b785f4b6c25d313b2472751c29deb4b0170

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-11-09 18:47:22 +1030

      Commit message:


	  
		 Version bump after bugfix
 
    
  
    
      Package: ngsReports

      Commit: 078c11eb59ffebb740f84714c42cf3d64df33d0a

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-11-09 18:28:18 +1030

      Commit message:


	  
		 Bugfix in cutadapt parsing
 
    
  
    
      Package: miaViz

      Commit: 894e603170b4b9fc397022df2970a87675fe0249

      Author:  Muluh <127390183+0xMuluh@users.noreply.github.com> 

      Date: 2025-11-09 10:01:57 +0200

      Commit message:


	  
		 #197 plotRDA (#200)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 
    
  
    
      Package: BulkSignalR

      Commit: e236c5a672c11179cd6849c10309823429230d15

      Author:  jcolinge <65902924+jcolinge@users.noreply.github.com> 

      Date: 2025-11-08 23:09:36 +0100

      Commit message:


	  
		 bug-fix: multtest does not work with len 1 vectors
 
    
  
    
      Package: basilisk.utils

      Commit: 863ddfbb45c346e458764d3fb57802ba77b07ba9

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-11-09 08:33:51 +1100

      Commit message:


	  
		 Commented on the naming situation in the vignette.
 
    
  
    
      Package: GSVA

      Commit: 51b250c28b4b2b80b1e480d16a7c7009b8bec37c

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-08 19:12:38 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: GSVA

      Commit: 5c5fb30bce9feee0e9988855eb7761db727d3a13

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-08 19:12:15 +0100

      Commit message:


	  
		 Fix in kcdf="Gaussian" when input is SparseArray
 
    
  
    
      Package: SingleCellSignalR

      Commit: 926b6b567118158543b51741aa21f4a1c53d943e

      Author:  jcolinge <65902924+jcolinge@users.noreply.github.com> 

      Date: 2025-11-08 18:13:31 +0100

      Commit message:


	  
		 bug-fix: syntax error in message()
 
    
  
    
      Package: SingleCellSignalR

      Commit: e427e35f9ead3db8eba6eb210ded0ccb9b8a2306

      Author:  jcolinge <65902924+jcolinge@users.noreply.github.com> 

      Date: 2025-11-08 17:50:50 +0100

      Commit message:


	  
		 syntax error in message()
 
    
  
    
      Package: SparseArray

      Commit: 45142ef19371007d50ea723ddb3527dd3ebb2fea

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-08 01:29:02 -0800

      Commit message:


	  
		 start refactoring C-level helper subassign_leaf_by_OPBuf()
 
    
  
    
      Package: SparseArray

      Commit: 0fa8490006d8d89715b57255a3ef24137cb4e863

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-07 22:05:39 -0800

      Commit message:


	  
		 more improvements to internal helper .subassign_SVT_with_Rarray()
 
    
  
    
      Package: crisprDesign

      Commit: afa77b0961499c0f7b5e87b8e5dcc6006e19d432

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-07 14:00:14 -0800

      Commit message:


	  
		 Merged news
 
    
  
    
      Package: crisprDesign

      Commit: 9d8923b8f1b7af9811dac905a55df7d757f7d3ce

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-07 13:59:01 -0800

      Commit message:


	  
		 Added more annotation columns to addEditedAlleles
 
    
  
    
      Package: crisprDesign

      Commit: 30c99479f710a898ff6b0e24e0d0cfc11603e61c

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-07 12:05:59 -0800

      Commit message:


	  
		 Added aa changes column
 
    
  
    
      Package: crisprDesign

      Commit: e512a93960f543552628e12cb24c10838ebdf573

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-05 15:50:23 -0800

      Commit message:


	  
		 Fixed .addAminoAcids
 
    
  
    
      Package: crisprDesign

      Commit: ab013fff6a41e3b84e20e5e63e50a403133c1b44

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-05 09:54:48 -0800

      Commit message:


	  
		 Done with the be vignette
 
    
  
    
      Package: crisprDesign

      Commit: f8b4ffaf9cf02275aa54b0b3231005e8d05a9b72

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-05 09:53:56 -0800

      Commit message:


	  
		 Updated gitignore
 
    
  
    
      Package: crisprDesign

      Commit: cd79f12415bf0aa5ff3cd9b09008728ecfbc43ca

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-05 09:30:52 -0800

      Commit message:


	  
		 Fixed scoring one more time
 
    
  
    
      Package: crisprDesign

      Commit: b0c65bf4275531e8f7424508b362dc6c892351f7

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-04 19:06:57 -0800

      Commit message:


	  
		 Finalized new variant calling algorithm
 
    
  
    
      Package: crisprDesign

      Commit: f251158351d27a6138fcff0faac59026ca542012

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-04 10:29:14 -0800

      Commit message:


	  
		 Added maxVariantScore back
 
    
  
    
      Package: crisprDesign

      Commit: c792e561a60948d17ea4046c7b5ffd6027949ef3

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-11-03 15:00:15 -0800

      Commit message:


	  
		 Simplified the editing algo
 
    
  
    
      Package: crisprDesign

      Commit: fc94df1559fa31b66bccc23e3fc4fda299596ac0

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-31 12:13:07 -0700

      Commit message:


	  
		 Dealing with unassigned
 
    
  
    
      Package: crisprDesign

      Commit: a690ab62fed4ab1d0a283de6a09436a6626bf091

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-31 11:25:54 -0700

      Commit message:


	  
		 Adding amino acids for non-editing alelles
 
    
  
    
      Package: crisprDesign

      Commit: cbc2ea7a13ba7875d9780628605275bf55f8b247

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-30 16:38:56 -0700

      Commit message:


	  
		 Added aa position to editedAlleles
 
    
  
    
      Package: crisprDesign

      Commit: 6e255356f05fd37d313453eb4674029727ecc2f6

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-30 15:59:37 -0700

      Commit message:


	  
		 Added position information to editedAlleles
 
    
  
    
      Package: crisprDesign

      Commit: c4c33a6be17f4c730d41354bea73f7b0d03bd976

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-30 15:09:16 -0700

      Commit message:


	  
		 Done
 
    
  
    
      Package: crisprDesign

      Commit: c956a94039d1354ae8407612bef009c5e5227d99

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-30 10:10:21 -0700

      Commit message:


	  
		 Removed missenseMargin
 
    
  
    
      Package: crisprDesign

      Commit: b70fb06e57e0236594e0c6de0dc04aba9947159c

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-29 11:18:39 -0700

      Commit message:


	  
		 Added no editing category
 
    
  
    
      Package: crisprDesign

      Commit: b9b8a33de5e89ee2a0ed791999fb8b5df453bc7e

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-29 11:10:14 -0700

      Commit message:


	  
		 Fixed editedAlleles accessor function unlisting option
 
    
  
    
      Package: crisprDesign

      Commit: a954d5708eeab6817ba65b6b2e03074d0b2d7ee2

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-28 10:18:02 -0700

      Commit message:


	  
		 Added splice junction call for BE
 
    
  
    
      Package: crisprDesign

      Commit: 5f14e7346aec0cedf7ff958dcbba86f277dd5da8

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-27 21:08:49 -0700

      Commit message:


	  
		 Done with the missense
 
    
  
    
      Package: crisprDesign

      Commit: 5738cbf38fbfa8ca56fd6891ada66a0ead456070

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2025-10-27 18:43:34 -0700

      Commit message:


	  
		 Added a few modifications to the allele calling
 
    
  
    
      Package: lefser

      Commit: ffb1ed63daa7a5f75e80b820032b22cb691e1313

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 15:43:02 -0500

      Commit message:


	  
		 version bump 1.21.1
 
    
  
    
      Package: lefser

      Commit: b6127082808619eefb081659c2b98bffc6043099

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 15:45:34 -0500

      Commit message:


	  
		 add label.font.color to vignette
 
    
  
    
      Package: lefser

      Commit: f897658cd8d6c3120b6970b26bb28d3683cee2d1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 15:45:17 -0500

      Commit message:


	  
		 update NEWS.md
 
    
  
    
      Package: lefser

      Commit: 94dfba8e6b3a34e0ff07e79f1bc4d3025dc840fe

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 15:20:09 -0500

      Commit message:


	  
		 fix color argument defaults

- improve .selectPalette
 
    
  
    
      Package: lefser

      Commit: 11857b7c528c5efc267088ca90041d14a405b521

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 14:30:43 -0500

      Commit message:


	  
		 fix code and doc formatting
 
    
  
    
      Package: lefser

      Commit: 2c3d96b90e6670539ff5b55a9f006caca14a0674

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 14:25:07 -0500

      Commit message:


	  
		 add label.font.color and ... to lefserPlot
 
    
  
    
      Package: lefser

      Commit: d7b1cefab8d7768b660b94b3b97a4232e8a34418

      Author:  Copilot <198982749+Copilot@users.noreply.github.com> 

      Date: 2025-11-07 14:09:43 -0500

      Commit message:


	  
		 Add label.font.face parameter to lefserPlot() for text formatting control (#90)

* Add label.font.face parameter to lefserPlot function

Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>

* Add input validation for label.font.face and fix typo

Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>

* use match.arg

* update docs

* update unit test

* update NEWS

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>
Co-authored-by: LiNk-NY <marcel.ramos@sph.cuny.edu> 
    
  
    
      Package: SparseArray

      Commit: c445d0d8ea452af99f3bbcb84676c47eeae0658b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-11-07 11:46:58 -0800

      Commit message:


	  
		 more improvements to internal helper .subassign_SVT_with_Rarray()
 
    
  
    
      Package: cBioPortalData

      Commit: 0773368269dee2904f8c571c853281ca20f676b6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 13:23:07 -0500

      Commit message:


	  
		 version bump 2.23.2
 
    
  
    
      Package: cBioPortalData

      Commit: ae577da66f949aed81ca0c39d1dc9076e4c767f5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-07 13:21:15 -0500

      Commit message:


	  
		 bug fix: remove resourceCounts from API response
 
    
  
    
      Package: MetaScope

      Commit: d49e047678018638e05ac2266605c31ea1923fad

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-11-07 11:54:11 -0500

      Commit message:


	  
		 Resolve merge conflicts
 
    
  
    
      Package: MetaScope

      Commit: bca3bbb4963f7f5d3f13dfa4e2285caa65c845ae

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-11-07 11:43:38 -0500

      Commit message:


	  
		 checks bug fixes
 
    
  
    
      Package: MetaScope

      Commit: cd34616980c01e1fae35c32dc3efd0406941500e

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-11-07 11:14:55 -0500

      Commit message:


	  
		 check bug fixes
 
    
  
    
      Package: MetaScope

      Commit: 3d4c4ed378b77f9988fdde11ba725d2eee95a1b6

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-10-20 22:55:01 -0400

      Commit message:


	  
		 Merge pull request #57 from seanlu96/master

chunk update bam 
    
  
    
      Package: MetaScope

      Commit: 0f99183dfb2164cf63deb05e6b2f509697dee9a5

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-10-20 22:54:20 -0400

      Commit message:


	  
		 chunk update bam
 
    
  
    
      Package: MetaScope

      Commit: d557dbb562f4ee52ca9e2d8c8efc3a5111aec550

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-10-17 19:54:46 -0400

      Commit message:


	  
		 Merge pull request #56 from seanlu96/master

optimized metablast 
    
  
    
      Package: MetaScope

      Commit: c4d02fb5771be37f3a579f616c8a6e0bc9010725

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-10-17 19:54:19 -0400

      Commit message:


	  
		 Merge branch 'wejlab:devel' into master
 
    
  
    
      Package: MetaScope

      Commit: 36623210f8e6768b89fff038ca6a7a3ffa070055

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-10-17 19:53:35 -0400

      Commit message:


	  
		 metablast optimizations
 
    
  
    
      Package: MetaScope

      Commit: 886098a5fd8188dd3918fba17718417e13ff3534

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-10-16 14:51:22 -0400

      Commit message:


	  
		 Merge pull request #55 from seanlu96/master

fixed metablast 
    
  
    
      Package: MetaScope

      Commit: ff13ca697fc7d6b17ba6d1a1cf98718b69ad47b2

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-10-16 14:50:38 -0400

      Commit message:


	  
		 fixed metablast
 
    
  
    
      Package: MetaScope

      Commit: 354cfc580f9fe7de1f01d577d0590076fa765c7d

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-25 11:55:51 -0400

      Commit message:


	  
		 Merge pull request #54 from seanlu96/master

update run metascope 
    
  
    
      Package: MetaScope

      Commit: a7781ac522ae6867cb4e8d427a0cb487034eef41

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-25 11:55:32 -0400

      Commit message:


	  
		 Merge branch 'wejlab:devel' into master
 
    
  
    
      Package: MetaScope

      Commit: 70e44985ee146d01b4fa43e7aae1b47ab0b9cc55

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-25 11:55:25 -0400

      Commit message:


	  
		 Update run_metascope.R

added extra args for align_target 
    
  
    
      Package: MetaScope

      Commit: 608121a4be95d7655e4096deaaf0e26acd8458c1

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-24 12:53:37 -0400

      Commit message:


	  
		 Merge pull request #53 from seanlu96/master

update to generate merged feature tables 
    
  
    
      Package: MetaScope

      Commit: 48fcc2200a7115bcf1992203673f6bd5602765ae

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-24 12:52:18 -0400

      Commit message:


	  
		 Merge branch 'wejlab:devel' into master
 
    
  
    
      Package: MetaScope

      Commit: a3d1c718fe649446fbe2471d0b2da7ad35b3b27f

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-09-24 12:51:50 -0400

      Commit message:


	  
		 Merge branch 'master' of https://github.com/seanlu96/MetaScope
 
    
  
    
      Package: MetaScope

      Commit: 5d93b1e2be6c0a7b5151976481a1b07be57cfdd2

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-22 17:04:27 -0400

      Commit message:


	  
		 added merged feature table output for metascope
 
    
  
    
      Package: MetaScope

      Commit: 7ee2a8db86179e0218ff20a471361d429e62a659

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-22 17:04:52 -0400

      Commit message:


	  
		 Merge pull request #52 from seanlu96/master

updates to run_metascope 
    
  
    
      Package: MetaScope

      Commit: 371872fbca868ff63b87a0c4b33c8aa06630f1a0

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-22 17:04:27 -0400

      Commit message:


	  
		 Merge branch 'wejlab:devel' into master
 
    
  
    
      Package: MetaScope

      Commit: 831a011d0841cc9339ed2fe87ef25feefa59d45f

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-09-22 16:32:25 -0400

      Commit message:


	  
		 run_metascope bug fixes with arguments
 
    
  
    
      Package: MetaScope

      Commit: a1562173bf913492b6ba6218f91658c4bed20204

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-18 17:30:44 -0400

      Commit message:


	  
		 Update README.md 
    
  
    
      Package: MetaScope

      Commit: 1d60e6122fd0b0f1aecd7d6d49263c6ef38362fe

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-09-15 17:06:54 -0400

      Commit message:


	  
		 bug fixes
 
    
  
    
      Package: MetaScope

      Commit: 54f8e6a0402863398d489a0421fe93f008bedc17

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-09-15 16:34:44 -0400

      Commit message:


	  
		 added wrapper function for full metascope 16S
 
    
  
    
      Package: MetaScope

      Commit: face9eb7577f12edc845f08a7fb893fc5c1997fb

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-09-15 09:52:59 -0400

      Commit message:


	  
		 Merge pull request #51 from seanlu96/master

bug fixes with download_refseq 
    
  
    
      Package: MetaScope

      Commit: 426dfa7fa87a867807025e7d197c0177375efa33

      Author:  Sean Lu <seanlu96@gmail.com> 

      Date: 2025-09-05 13:43:26 -0400

      Commit message:


	  
		 bug fixes
 
    
  
    
      Package: MetaScope

      Commit: 445bf96b6d8c9833a502376485ce0752fc7449ff

      Author:  Sean <89270441+seanlu96@users.noreply.github.com> 

      Date: 2025-08-25 20:00:53 -0400

      Commit message:


	  
		 Merge pull request #50 from technophilic03/devel

Added metascope_inspect function as a wrapper to bowtie2-inspect 
    
  
    
      Package: MetaScope

      Commit: d5daa5a8cb28ef05331c3c6f086a27d978e5eb3d

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2025-08-25 12:54:03 -0400

      Commit message:


	  
		 Roxygen updates for metascope_inspect
 
    
  
    
      Package: MetaScope

      Commit: 76491985d2ac2c16a62f480016e8b76988320605

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2025-08-25 12:53:10 -0400

      Commit message:


	  
		 Added bowtie2 inspect scripts to inst/ folder
 
    
  
    
      Package: MetaScope

      Commit: 835a2fcaaa6800bb99f47140d5541cd68a1e7760

      Author:  technophilic03 <leng@bu.edu> 

      Date: 2025-08-25 12:52:02 -0400

      Commit message:


	  
		 Added metascope-inspect as a bowtie2-inspect wrapper
 
    
  
    
      Package: GSVA

      Commit: da6381b67ab5f664e767cecca96284fd867425e0

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-07 17:46:40 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: GSVA

      Commit: 8adda3da3de4b9d1d60f965fcae8bc05a205723d

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-07 17:46:16 +0100

      Commit message:


	  
		 Fix on the parallel scanning of nonzero constant rows
 
    
  
    
      Package: Aerith

      Commit: 5365565e471a2127ceb413ee125f625399ada945

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2025-11-04 17:09:34 -0600

      Commit message:


	  
		 bump version
 
    
  
    
      Package: Aerith

      Commit: 6f12a2d4d094cb5f96c6719c899ef69d9878f15c

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2025-11-04 17:02:43 -0600

      Commit message:


	  
		 fix citation
 
    
  
  


</div>

</div>