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GIT Logs

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

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Package: omXplore
Commit: 752c6a9ea3c0470373dcce20127920121d0b70d3
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-10-23 15:52:58 +0200
Commit message:

 Fix images not found
Package: omXplore
Commit: 5eb18669b041a6cc72780986a21cd188e5271f6d
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-10-23 15:52:13 +0200
Commit message:

 Fix images not found
Package: enrichplot
Commit: 281bbf15afb4de5640dff9a4b5abff2e50a2dece
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 21:40:09 +0800
Commit message:

 remove file
Package: enrichplot
Commit: 47c74b76ef04868f4616a2272e85316db1f55f8a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 21:37:54 +0800
Commit message:

 tidy code
Package: enrichplot
Commit: 354df17ec3724cb2bae13e94c317ceb76c741872
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 21:19:43 +0800
Commit message:

 Merge pull request #332 from ToledoEM/ggplot2_bump

Modernize ggplot2 usage (remove deprecated aes_string/aes_) and tidy up examples
Package: enrichplot
Commit: d7ab221b739110bd786e21b00784dc5ad7766c56
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 21:13:10 +0800
Commit message:

 update readme
Package: enrichplot
Commit: 8a53387cd6bc5f1969c1d95dc2594bec3b3ae489
Author: Enrique <ToledoEM@users.noreply.github.com>
Date: 2025-10-04 09:09:33 +0100
Commit message:

 Usage of ggplot2 code and examples

It replaces all uses of the deprecated aes_string() and aes_() helpers with tidy-eval friendly constructs (aes() + .data / .data[[...]])
Package: DESeq2
Commit: 5337ba15ae6e9c9aaa1874f088a96c6eb8ccef72
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-23 09:30:17 -0400
Commit message:

 add upshot docs, fix ggplot2 aes, bump version
Package: DESeq2
Commit: ac1d1e398d729a550e35114a0bc15e0195139000
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2025-10-23 09:13:40 -0400
Commit message:

 Merge pull request #120 from rrross/devel

Implementing greaterAbsUPSHOT
Package: DESeq2
Commit: 90c086b7296676761a9322a4d122298e1ee784f4
Author: rrross <57932933+rrross@users.noreply.github.com>
Date: 2025-10-22 23:46:52 -0500
Commit message:

 Add greaterAbsUPSHOT tests to test_results.R
Package: DESeq2
Commit: 8dcbe3e358b3ddc76f604c57ebdc4a75a3b5f029
Author: rrross <57932933+rrross@users.noreply.github.com>
Date: 2025-10-22 23:43:10 -0500
Commit message:

 Add greaterAbsUPSHOT to results.R
Package: omXplore
Commit: 1f4eda1f9913a4c6184ebc2483397391949fd001
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-10-23 15:25:07 +0200
Commit message:

 Fix images not found
Package: ChIPseeker
Commit: d7ebedb6f5d7f1addb29aa51e77ad12d72f5b1ad
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 20:46:20 +0800
Commit message:

 bump version
Package: ChIPseeker
Commit: fcc85bf4166cafd40ef6b51c272bc17cb00fbac2
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 20:44:15 +0800
Commit message:

 Merge pull request #263 from MingLi-929/devel

update txdb check function
Package: ChIPseeker
Commit: 8333c5b6f42b01cccf5a7e5e4e312cb69e6308b1
Author: liming <limiang929@gmail.com>
Date: 2025-10-23 18:22:50 +0800
Commit message:

 update txdb check function
Package: DaparToolshedData
Commit: 60c8fea3ea254e94cc7354dd952c1d6f8b85e13e
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-10-23 13:51:54 +0200
Commit message:

 Update examples
Package: DaparToolshedData
Commit: aafc24af6f5ad75e45a66ee25c1f2538defe2edd
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-10-23 13:20:02 +0200
Commit message:

 Bumpversion
Package: consICA
Commit: f64a7f660282432ed002c1741a5ddeba2fa6dc80
Author: Maryna Chepeleva <maryna.chepeleva@gmail.com>
Date: 2025-10-23 13:15:58 +0200
Commit message:

 + hot fix + bump version 2.7.5
Package: consICA
Commit: d06d36ce87af47303b453299309d1e38d66178e1
Author: Maryna Chepeleva <maryna.chepeleva@gmail.com>
Date: 2025-10-23 12:04:17 +0200
Commit message:

 [man][examples] Hot fix for CMD Check timeout on nebbiolo2 + bump version 2.7.4
Package: tidybulk
Commit: 35e34e7f9d79b62e85b04a8358a9eb32a77c70c3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-03 13:13:29 +0930
Commit message:

 update NEWS.rd
Package: tidySummarizedExperiment
Commit: 9f7c26e0519c92f9682b270d566da127367bcbc0
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-13 09:35:52 +1030
Commit message:

 Merge pull request #108 from tidyomics/query-to-slot-routines

Query to slot routines
Package: tidySummarizedExperiment
Commit: 79dcfd9692db0bab9c28551fb0fa92d2cd69715a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 16:29:20 +0930
Commit message:

 Remove deprecated tests for old vocabulary from the test suite to streamline codebase and improve maintainability.
Package: tidySummarizedExperiment
Commit: a10d0f0eebafdb768bde5cc94f977c4aed0d85e4
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 16:29:07 +0930
Commit message:

 Add NEWS
Package: tidySummarizedExperiment
Commit: 33d250469898a6b601fe3829b2099b7edebfd7c0
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 16:07:49 +0930
Commit message:

 Add 'airway' to DESCRIPTION suggests for improved functionality
Package: tidySummarizedExperiment
Commit: 728ece1e69f06bebdb3ca85ddb11ca2a235490a1
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 15:57:33 +0930
Commit message:

 Clarify usage of rename function in introduction vignette by specifying dplyr::rename for improved clarity in examples.
Package: tidySummarizedExperiment
Commit: 6b36fb72c9f7eb94da0cd2e4ad2fd4b2ddea9f12
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 14:16:46 +0930
Commit message:

 Update website links in introduction vignette to reflect new tidyomics domain
Package: tidySummarizedExperiment
Commit: caa3fcb48d3aba2f287d43d14d53b9a2a0f42b2d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 14:15:37 +0930
Commit message:

 Solve error for count() in vignette
Package: tidySummarizedExperiment
Commit: b0b7baba47c9addbc8e1167090c5d51bd9e9af0d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 14:04:22 +0930
Commit message:

 Update installation instructions and clarify usage of slice function in introduction vignette

Replace devtools with remotes for GitHub installation and specify dplyr::slice for clarity in the examples. This enhances the documentation for better user guidance.
Package: tidySummarizedExperiment
Commit: 5d4de8bc51655c6f991ba2c124219619011f651f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-02 13:57:34 +0930
Commit message:

 Moving benchmark vignette to dev
Package: tidySummarizedExperiment
Commit: ee7aacde03b71e2314d72f151bd76ec5e7791e1d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 18:49:43 +0930
Commit message:

 Merge branch 'master' into query-to-slot-routines
Package: tidySummarizedExperiment
Commit: 6ccebeb0b4819ca03a0501025a743282931191a3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 16:38:48 +0930
Commit message:

 Add caching mechanism for benchmark results in the scoping vignette

Introduce a parameter to enable caching of benchmark results, improving efficiency by loading existing results from a file if available. This change enhances the performance of the benchmarking process and reduces redundant computations.
Package: tidySummarizedExperiment
Commit: 948726979f7dc5ec00ccb85dfc0f8ae6788ad9bf
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 16:36:39 +0930
Commit message:

 fix CHECKS
Package: tidySummarizedExperiment
Commit: 94cdc85e6432a30532283f41971be4662526e769
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 09:59:58 +0930
Commit message:

 Add left_join documentation and examples for SummarizedExperiment
Package: tidySummarizedExperiment
Commit: 9ae788d35e959fbdd6c2dd9965c0511f72ef825c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 09:53:52 +0930
Commit message:

 Remove deprecated select.SummarizedExperiment function and associated comments from dplyr_methods.R to streamline the codebase. This change enhances clarity and prepares for future improvements in column selection functionality.
Package: tidySummarizedExperiment
Commit: 5a9de752540224e84d28f088352d1c16f2e2ee9d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 09:53:15 +0930
Commit message:

 Rename scoping vignette
Package: tidySummarizedExperiment
Commit: 79e644585cbd4bbc9f04a7ad08ebaf38e0716c95
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 09:52:30 +0930
Commit message:

 Add select functionality with scope analysis for SummarizedExperiment

Introduce a new select.SummarizedExperiment function that allows users to select columns from colData, rowData, and assays while analyzing the scope of the selection. Implement an internal function, analyze_query_scope_select, to determine the domains affected by the selection. Add comprehensive tests to validate the new functionality and ensure correct metadata reporting. Update the benchmark vignette to include select scenarios, enhancing the overall usability and performance of the package.
Package: tidySummarizedExperiment
Commit: 29019fd0773104062b8fcd86b20ef6a7d13789f3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-01 00:05:06 +0930
Commit message:

 Refactor join functions

Update the join_efficient_for_SE function in join.R to improve clarity and efficiency in join operations. Modify comments for better understanding and remove unnecessary lines. Enhance test cases for left_join, inner_join, right_join, and full_join to ensure accurate metadata reporting of join scopes. Clean up unused code in test files to streamline the testing process.
Package: tidySummarizedExperiment
Commit: eb90a120a7a297de55bc32c43b976b4eeabafb9f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 23:04:48 +0930
Commit message:

 Refactor join methods for SummarizedExperiment and add new join utility functions

Remove deprecated join methods from dplyr_methods.R to streamline the codebase. Introduce a new join utility function, join_efficient_for_SE, in join.R to handle various join operations efficiently based on the scope of join keys. Update tests to validate the functionality of left_join, inner_join, right_join, and full_join for SummarizedExperiment, ensuring comprehensive coverage and improved performance.
Package: tidySummarizedExperiment
Commit: b7e5f7f4a2e400ab7fb57801f5a181b76f5d97b5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 23:03:56 +0930
Commit message:

 Remove  filter and join methods from dplyr_methods.R
Package: tidySummarizedExperiment
Commit: 7d3564465321bfc03d627baf40afcd8c0af10a42
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 23:03:26 +0930
Commit message:

 Add rename functionality

Remove deprecated filter and join methods from dplyr_methods.R, streamlining the codebase. Introduce a new rename.SummarizedExperiment function in rename.R, enhancing the ability to rename columns in colData and rowData while ensuring proper handling of special/view-only columns. This update improves the overall functionality and usability of the package.
Package: tidySummarizedExperiment
Commit: 3c4d1ad73459535509022dea6431b575dc190033
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 22:36:18 +0930
Commit message:

 Add analyze_query_scope_filter function and integrate into filter.SummarizedExperiment

Introduce the analyze_query_scope_filter function to assess the scope of filter queries, determining whether they target colData, rowData, or assays. Integrate this analysis into the filter.SummarizedExperiment function to enhance its capability in handling mixed operations. Additionally, remove the previous implementation of analyze_query_scope_filter from query_scope_analysis.R to streamline the codebase. Update tests and vignettes to reflect these changes and ensure comprehensive coverage of new filtering functionalities.
Package: tidySummarizedExperiment
Commit: 2b9788321892f9c49c2501e7ea0a9d1ec1df447f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 22:30:08 +0930
Commit message:

 Enhance filter functionality with scope analysis and decomposition

Refactor the filter.SummarizedExperiment function to support decomposition of filter queries and analyze the scope of filtering operations. Introduce a new internal function, analyze_query_scope_filter, to determine whether filters target colData, rowData, or assays. Update the modify_se_plyxp function to handle additional arguments, improving flexibility. Additionally, add comprehensive tests to validate the new features and ensure correct scope reporting in metadata.
Package: tidySummarizedExperiment
Commit: fd8e9dbc338ade0bae38842888ff00e77992b636
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 21:43:30 +0930
Commit message:

 Add benchmark vignette for `mutate()` performance comparison

Introduce a new vignette titled "Speed-up `tidySummarizedExperiment` with `plyxp`" that benchmarks various `mutate()` scenarios across two branches of the repository. The vignette outlines the motivation, design principles, and setup for running benchmarks, including helper functions and visualization of results. This addition supports ongoing efforts to enhance the performance of `mutate()` operations in the `tidySummarizedExperiment` package.
Package: tidySummarizedExperiment
Commit: 9bd3589a770ff86d3eaa64e81636060bb6ec2afd
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 19:42:09 +0930
Commit message:

 version UP
Package: tidySummarizedExperiment
Commit: b3cd45aa5403c981cfc78fc964bc6d0f68b94a14
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 17:36:30 +0930
Commit message:

 version UP
Package: tidySummarizedExperiment
Commit: 4fa1e02424c9878f01b85cd25bb823e94cc8b2e7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 17:21:54 +0930
Commit message:

 Enhance mutate.SummarizedExperiment to record latest mutate scope

Update the mutate.SummarizedExperiment function to store the latest mutate scope report in the metadata of the result. This addition facilitates testing and introspection of the mutate operations, improving the overall functionality and usability of the mutate feature.
Package: tidySummarizedExperiment
Commit: 0fbadb672e3dfdf1d994ec1eaabf87d8e3a8285f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 17:21:13 +0930
Commit message:

 Add comprehensive tests for mutate function in SummarizedExperiment

Introduce a new test file for the mutate function, covering a wide range of scenarios including simple and complex operations on colData, rowData, and assays. The tests validate functionality, scope detection, error handling, and integration with other dplyr operations, ensuring robust performance and accuracy in various use cases.
Package: tidySummarizedExperiment
Commit: 92072d71f9d3b9a82cfc5fdced8e52477c44d80f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 15:07:08 +0930
Commit message:

 Enhance mutate functionality with new decomposition and analysis features

Introduce a new function, decompose_tidy_operation, to handle the decomposition of dplyr operations into individual steps for better analysis. Update the mutate.SummarizedExperiment function to utilize this new decomposition approach, improving the handling of mixed scope operations. Additionally, add a new utility function, map_to_plyxp, to convert mixed scope expressions into plyxp form for efficient execution. This update enhances the flexibility and performance of mutate operations across various data types.
Package: tidySummarizedExperiment
Commit: fbc380076b8a6445e670ff6e6fcb25aadcca264f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 14:44:59 +0930
Commit message:

 Refactor mutate.SummarizedExperiment to streamline scope handling

Revise the mutate.SummarizedExperiment function to improve scope handling by consolidating logic into a single case_when structure. Introduce a new internal helper function, mutate_via_tibble, for efficient tibble conversion during mutations. This update enhances code clarity and maintains functionality across various data types.
Package: tidySummarizedExperiment
Commit: 65433ab50fe748ef133129630cb6d8b8d720ff3a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 14:37:57 +0930
Commit message:

 Implement mixed scope handling in mutate operations

Enhance the mutate.SummarizedExperiment function to support mixed scope operations by introducing a new helper function, modify_se_plyxp, which converts expressions to plyxp form for efficient execution. Add a utility function, convert_to_plyxp_form, to handle the conversion of colData and rowData references. This update improves the flexibility and performance of mutate operations involving multiple data types.
Package: tidySummarizedExperiment
Commit: 3ee1298f91ee792c430c35fe3586314bb42afc54
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 12:33:39 +0930
Commit message:

 Add dependency analysis for query scope in analyze_query_scope_mutate

Enhance the analyze_query_scope_mutate function to include a new dependency analysis step that detects mixed operations in mutate expressions. Introduce analyze_expression_dependencies function to evaluate the scope of variables referenced in expressions, determining if they span multiple data types (assays, colData, rowData). This addition improves the accuracy of query scope analysis by allowing for more nuanced handling of mixed data types.
Package: tidySummarizedExperiment
Commit: 7a2a77c1145d4ce350c905d0cf22c8e42c386c64
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 11:52:33 +0930
Commit message:

 adapt rename
Package: tidySummarizedExperiment
Commit: 338de95d08e16ba3e5c52ffd429435191e1747e7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 11:22:33 +0930
Commit message:

 Refactor mutate functionality in SummarizedExperiment by renaming mutate_features and mutate_samples to modify_features and modify_samples, respectively. Introduce a new helper function, mutate_assay, for handling assay-only mutations. Add query scope analysis functions to determine the target data types for mutate operations. Remove deprecated documentation for the old mutate functions.
Package: tidySummarizedExperiment
Commit: 62b5917c9fc68545422756a79b8d688149829d1f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-30 18:33:14 +0930
Commit message:

 Add functions to extract column and row data from mutated tibbles, and refactor update_SE_from_tibble to utilize these new functions. Include tests for the new extraction functions to ensure correct functionality.
Package: sccomp
Commit: c6f2afe04ce0870ffb2225fcd1453270ccd94bcd
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-15 11:33:59 +1030
Commit message:

 Merge pull request #236 from MangiolaLaboratory/fix-deprecated-arguments

 Remove deprecated .sample argument handling in sccomp_estimate funct…
Package: sccomp
Commit: 4c5774cdb1932ae02e4c17fe0387dff1f07dbccc
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-15 10:02:57 +1030
Commit message:

  Remove deprecated .sample argument handling in sccomp_estimate function and add tests for old argument style compatibility.
Package: scDblFinder
Commit: d847f68794adb3a7a4e61f7ba5d7fefe29d1568d
Author: plger <pl.germain@gmail.com>
Date: 2025-10-23 09:46:31 +0200
Commit message:

 try getting rid of namespace warning
Package: graphite
Commit: eb4b1de5cdebaa3787b08a5c49fdd95b088ee115
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-23 11:24:01 +0200
Commit message:

 Label for vignette chunk
Package: graphite
Commit: 592ddb671b25e5afee6fbd71d07ff3173d6eda26
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-23 10:36:44 +0200
Commit message:

 ORCID for package maintainer
Package: graphite
Commit: d55703144236640de9108ed9e384ec0941225158
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-23 10:19:00 +0200
Commit message:

 Enable BiocCheck for vignettes
Package: graphite
Commit: b944c420237e180219a48ef68c8c0a6fdd1e1840
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-23 10:05:22 +0200
Commit message:

 Disable BiocCheck for man pages
Package: MetNet
Commit: bf52d3fdf3019e98b449f6d1c95e80872711d108
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-23 10:59:09 +0200
Commit message:

 bump version to 1.27.3 in devel
Package: MetNet
Commit: 6b8cacd77812a6ebbb4f8edf89b6f5e74df70a1e
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-23 10:55:59 +0200
Commit message:

 bug fix: add diag values of 1 to adj
Package: epiregulon
Commit: c8e0c5ed0b5c429ef384b436579bc8080649caee
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-23 08:09:28 +0000
Commit message:

 v1.99.5
Package: epiregulon
Commit: 136b473802a59ff4d80108a1fe02b10ec7aeeffa
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-23 08:08:50 +0000
Commit message:

 handle nested matrix in DFrame
Package: epiregulon
Commit: 72915962a6e6f7b2b379cc8d82d2596a0e557d16
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-23 08:07:46 +0000
Commit message:

 correct typo
Package: ggtree
Commit: f872a3b338749fa29cfcb37e8fc6d03b3640ecc0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-23 16:04:45 +0800
Commit message:

 update
Package: BatChef
Commit: 02fe8d15c86ea2ed350b709428841b2ff7ad2a53
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-23 09:37:42 +0200
Commit message:

 Bump version: 0.99.6
Package: BatChef
Commit: 227a82a49131928d3cfa34f81184d85c603e6269
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-23 09:35:36 +0200
Commit message:

 Removed BatChef.Rproj from Git tracking
Package: BatChef
Commit: c8fa2ab5874090caf0312eb571987f0a9316d7d6
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-23 08:35:24 +0200
Commit message:

 Bump version: 0.99.5
Package: BatChef
Commit: 9f2138852ecef0daa68df92353b2e932073f4fa4
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-23 08:34:54 +0200
Commit message:

 Edit README.md
Package: BatChef
Commit: 18995fba50af3e8dd899608383bfbb7219030ef8
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-22 19:13:25 +0200
Commit message:

 Use \link{} in the documentation
Package: BatChef
Commit: 78369fd982753896221aac86377511d0a22d57b7
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-22 17:12:08 +0200
Commit message:

 Force conversion of AnnData object
Package: BatChef
Commit: a9e7cb5b5a9465d0eb122799c514ef1cb88a7376
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-22 17:11:29 +0200
Commit message:

 Ignore some warnings generated by IntegrateLayers()
Package: BatChef
Commit: ed0617a1ed20322c0c8da7dc4576ef79bd324c99
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-20 16:30:37 +0200
Commit message:

 Remove LazyData and add R (>= 4.1.0)
Package: BatChef
Commit: 4a922e2f9e6a740564cf7d57e6f3d7b500600f9a
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-20 16:29:03 +0200
Commit message:

 Suppress graphic for scMerge2 method
Package: BatChef
Commit: 9e6e41a07b3b02d8942a4f1405c952af0e18b643
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-16 11:34:28 +0200
Commit message:

 Delete python correction methods
Package: BatChef
Commit: 448816d77efc406a9f66d83c0405ca909dbf5931
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-16 09:31:10 +0200
Commit message:

 Document the recent changes in NEWS.md file
Package: anglemania
Commit: ddf0fb8efed173f7f15ebb3c3e6c58e4fb2bac34
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-10-23 08:30:27 +0200
Commit message:

 bump version
Package: anglemania
Commit: 6d00f7fbae2490e489229fe6f993119bd7d214a5
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-10-14 11:08:19 +0200
Commit message:

 implement single ranking instead of having two cutoffs
Package: anglemania
Commit: 6dd9bc404c58281d03e2402eda6acbdbfd7aa2b1
Author: Aaron Kollotzek <94226821+kollo97@users.noreply.github.com>
Date: 2025-09-24 10:38:03 +0200
Commit message:

 Update R-CMD-check.yaml, remove oldrel until it updates to R>=4.5.0
Package: anglemania
Commit: b7817ebdad041e3ad519582a3b8d4ab1d6b04274
Author: Aaron Kollotzek <94226821+kollo97@users.noreply.github.com>
Date: 2025-09-24 10:32:06 +0200
Commit message:

 Update R-CMD-check.yaml, remove oldrel until it updates to R>=4.5
Package: lcmsPlot
Commit: 4a5ace2a7a6ecc1808e6c4440d737b5126a0ff97
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-23 07:01:47 +0100
Commit message:

 chore: Add vignette figures options
Package: StatescopeR
Commit: 874934f94d1bd22277d75c237badd57a803545b3
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-10-23 08:06:04 +0200
Commit message:

 Small bug fix in BLADE deconvolution
Package: bluster
Commit: 8ba985737b656b9c3f41b34f8a989df66c23268b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-22 21:36:31 -0700
Commit message:

 Zero the lower-triangular part of the modularity ratio matrix.

This is primarily for compatibility with the latest version of igraph, which
doesn't like NAs in the adjacency matrix, even if it is explicitly told to
ignore the lower-triangular part.

Also removed some references to deprecated igraph functions.
Package: OSCA.advanced
Commit: 5e6af597f0654c71fd42a04b65d492134a0ba736
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-10-23 14:34:55 +1100
Commit message:

 Version bump
Package: OSCA.advanced
Commit: 53d7bc5484dcd4a6eb5a1a35e019804ac7188ca0
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-10-23 14:33:35 +1100
Commit message:

 Update protein-abundance.Rmd

- Switch to `SerialParam()` in `mumosa::findTopCorrelation()` to avoid crashes on macOS (aarch64)
- See https://github.com/OSCA-source/OSCA.advanced/issues/22 and https://github.com/LTLA/mumosa/issues/8
- Testing on Ubuntu (x86_64) where parallelisation works, the speed-up is fairly minor so this switch shouldn't cause timeout issues
Package: tidyprint
Commit: 76a91df2b073e847f16d5f01db09bc1d6f3bc6bc
Author: Chen Zhan <chen.zhan@adelaide.edu.au>
Date: 2025-10-23 12:06:58 +1030
Commit message:

 Bump version to 0.99.5 - Fix missing \value section in package man page

- Added @return section to tidyprint-package.R
- Regenerated man page documentation
- Fixed Bioconductor documentation warning
Package: tidyprint
Commit: b726aaf5cee86cb8526b92dcabee41bda3056243
Author: Chen Zhan <chen.zhan@adelaide.edu.au>
Date: 2025-10-23 11:49:07 +1030
Commit message:

 Bump version to 0.99.4 - Address reviewer comments

- Added comprehensive Introduction section to vignette with Bioconductor motivation
- Created NEWS file in correct Bioconductor format
- Added package-level documentation (tidyprint-package.Rd)
- Fixed vignette section numbering (removed decimal numbering)
- Ensured all exported functions have complete man pages
Package: tidyprint
Commit: a912b380ffbb8efd75c90e576b8e05fbb59ad957
Author: Chen Zhan <chen.zhan@adelaide.edu.au>
Date: 2025-10-23 10:06:02 +1030
Commit message:

 documation updates
Package: zellkonverter
Commit: b3b2dfb52349f0b7162c6225c7ec3bed42fd3e6f
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-23 01:28:37 +0200
Commit message:

 Update release notes
Package: zellkonverter
Commit: cb911e9a72ddb0d03880768ff4235192b2e54334
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-23 01:18:33 +0200
Commit message:

 Bump version and update NEWS
Package: zellkonverter
Commit: d712d4b8711d01e36f21f6f752de599714a8ffcb
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-23 01:16:35 +0200
Commit message:

 Bump roxygen version
Package: zellkonverter
Commit: 7246375223c3f1a4e60328cfc692856fcd588906
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-23 01:15:31 +0200
Commit message:

 Add anndata 0.12.3 environment
Package: zellkonverter
Commit: 8c0e2c61b37de15c613799125711ee21d0851322
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-22 21:02:43 +0200
Commit message:

 Add GitHub to authors
Package: zellkonverter
Commit: 4c9e346fddbdd628ce6705c6286b74faa4275007
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-22 21:01:07 +0200
Commit message:

 Add anndataR recommendataion message
Package: zellkonverter
Commit: a1f81b51ffb9706fa5d5a33084fbd3110a7dd859
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-08-26 07:18:19 +0200
Commit message:

 Merge pull request #150 from theislab/dependabot/github_actions/actions/checkout-5
Package: zellkonverter
Commit: 62fde73244751b9e8bfd1f1f19d21bd6062d9e7c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-08-25 15:02:57 +0000
Commit message:

 Bump actions/checkout from 4 to 5

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Package: scrapper
Commit: c954600ee23f6259ee9e7623f4f8515b16f8ce86
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-22 16:05:06 -0700
Commit message:

 Skip missing names in gene sets for scoreGeneSets, aggregateAcrossGenes.

Also skip duplicated gene names without error in aggregateAcrossGenes.
Package: dorothea
Commit: 08957d7c994e6712008f92307139572bbe174180
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 16:14:38 -0700
Commit message:

 dorothea 1.21.0

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeInfoDb
to the new Seqinfo package).
Package: visiumStitched
Commit: 96538cada41552ffe7e9ce0bb85558cce8f7442f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 15:29:54 -0700
Commit message:

 visiumStitched 1.1.3: No need to depend on GenomeInfoDb

The 'R CMD check' error on nebbiolo2 had to do with an issue with
the updateObject() method for GRanges objects that I fixed today
in GenomicRanges 1.61.6. Sorry for the inconvenience!
Package: pRoloc
Commit: e57c71b1abd187503fabbb65240b3a7007f75b61
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-10-22 22:47:51 +0100
Commit message:

 bump version
Package: pRoloc
Commit: 04d3b858b9c35ac03b4bef7098356d66e9351b6b
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-10-22 22:46:31 +0100
Commit message:

 fix tagm-mcmc unit tests
Package: pRoloc
Commit: 06dc55da1f7b60cd12e3e726bd60a445221f90e9
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-10-22 22:42:13 +0100
Commit message:

 ignore platform specific files
Package: StatescopeR
Commit: c4a7fb0f6fb259ad1a58546664a66f84a8b90d9f
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-10-22 23:43:54 +0200
Commit message:

 Minimized all examples and vignette for RMD check speed on nebiolo
Package: graphite
Commit: 8daee4cbaa8235c3890422f934a231b24197ee15
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-22 22:08:53 +0200
Commit message:

 Export purgeCacheV1()
Package: graphite
Commit: 987e672aa35134ac3fb91a11fc26e871f1afb21b
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-22 21:59:08 +0200
Commit message:

 Reinstate clipper support
Package: StatescopeR
Commit: 3905acbafdbfa6cc453a78801da20324a4022353
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-10-22 23:20:38 +0200
Commit message:

 Added readme
Package: StatescopeR
Commit: 91fbf36ca3d82308b0116e9e611a20b1f74264ad
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-10-22 22:34:59 +0200
Commit message:

 Revisions based on https://github.com/Bioconductor/Contributions/issues/3838#issuecomment-3261548846
Package: graphite
Commit: b14936299738c3bd8ae1d4fbafc11d1fbd1493a0
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-22 21:29:07 +0200
Commit message:

 Metabolite conversion based on equivalence classes
Package: graphite
Commit: f7be0621837fe2a81eff1753e18913a518fab923
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-22 15:51:28 +0200
Commit message:

 Update pathway data
Package: graphite
Commit: 38d3b9826efbc25f2f49a3750de5eca35c47a445
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-22 15:33:16 +0200
Commit message:

 Run CI against bioc-devel
Package: graphite
Commit: 9e45db6768ff8443be03e750eb118105df9513b3
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2025-10-22 12:59:30 +0200
Commit message:

 Automatic cleanup of stale pathway data
Package: OSTA
Commit: b766e49bebfa1986d06cd33676d8991cd1c876c7
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-22 15:46:04 -0400
Commit message:

 version and date
Package: OSTA
Commit: a4de653579c0e3a0dd8766340e8b282007d6ea4d
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-22 15:45:49 -0400
Commit message:

 check for existing Miniconda installation and update
Package: motifStack
Commit: e6e455d290c76250405d40b15382647051540c8b
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-22 15:25:40 -0400
Commit message:

 support hocomoco format import.
Package: SETA
Commit: dbdfac5f0048ac59879ce0fa212ab8bd2f6f9bba
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-10-22 21:12:35 +0200
Commit message:

 nebbiolo glmnet issues
Package: Uniquorn
Commit: 55a0342bd559018238a1f4b2e15ff21e258dedf3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 11:58:39 -0700
Commit message:

 Uniquorn 2.29.2: Several fixes

- Fix file name extension of all the RDS files contained in the package.
  Now .rds is used instead of .RData (the latter is for files created
  with save() which uses a different format).

- Update the GRanges objects contained in these .rds files to reflect
  the new location of the Seqinfo class definition (the class was
  recently moved from GenomeinfoDb to the new Seqinfo package).

- Drop dependency on GenomeInfoDb (not needed).

- Other minor cleanups in DESCRIPTION file.
Package: DspikeIn
Commit: 27573e45cad851c4b27f3b86af962055a2b168b9
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 20:23:04 +0200
Commit message:

 Add Classification to biocViews for machine learning context
Package: DspikeIn
Commit: e389965605c0b2e5f7ec90d45f85c087ba5b6277
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 20:07:36 +0200
Commit message:

 Wrap DESeq2 example in donttest to prevent Rdb error on build servers
Package: peakCombiner
Commit: 9cc7bab0937e87d5d2b51493fbb4a2cfe97a9b26
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 10:55:18 -0700
Commit message:

 peakCombiner 0.99.603: Move GenomeInfoDb from Imports to Suggests
Package: DspikeIn
Commit: 155b0b3c100494a2fb36b06d8e05c78d51e5f2da
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 19:55:22 +0200
Commit message:

 Add skip_on_bioc() to DESeq2 test to prevent TIMEOUT
Package: mitoClone2
Commit: 57551ab6f067b6821c6d0dea84b472610aadfd42
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 10:37:16 -0700
Commit message:

 mitoClone2 1.15.4: Update serialized GRanges instances **again**

Already did it in June in mitoClone2 1.15.1 (commit dba690a) but previous
commit (b0e29b8, Oct 18) by package maintainer reverted that.

IMPORTANT NOTE to package maintainer Story Benjamin: please make sure
to always resync your package repository on GitHub with your package
repository at git.bioconductor.org before making/pushing changes to
your package. Thanks!
Package: DspikeIn
Commit: 842fd31548a028a862b19dc95f0795bdccb35555
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 19:42:33 +0200
Commit message:

 Bump version to 0.99.27 after removing .DS_Store
Package: DspikeIn
Commit: 0464993001dfb93b53d41f19cf28b183da0fade0
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 19:42:33 +0200
Commit message:

 Remove all .DS_Store artifacts and ignore them
Package: scrapper
Commit: 4e75e61b9c14aa0060858113c836f7c0b7a7e3b9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-22 09:47:09 -0700
Commit message:

 Bugfix for the argument name.
Package: DspikeIn
Commit: 91be6a8311519cff1deabab4c2ec4801a8f2456c
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 19:04:04 +0200
Commit message:

 Describe your update briefly
Package: BiocPkgTools
Commit: 0ad4df332d6847d4f99075a39be441aac83cdb87
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 13:02:48 -0400
Commit message:

 version bump 1.27.14
Package: BiocPkgTools
Commit: 12339517e944d6840451db3a5fec45e9eddd2fb3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 13:02:36 -0400
Commit message:

 update Roxygen version
Package: BiocPkgTools
Commit: 0961068aa8c01ef8bb534fc1917cf8e1ae6daa1d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 13:02:23 -0400
Commit message:

 minor Rd formatting
Package: BiocPkgTools
Commit: e1971df7fe145019e766cd3441ad1b6b324f44f6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 13:02:13 -0400
Commit message:

 update version and pkgType arg docs
Package: BiocPkgTools
Commit: 7d59489311dcf590b9086347558bef59e53ef5d1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 13:01:32 -0400
Commit message:

 export biocVIEWSdb
Package: enhancerHomologSearch
Commit: 714767d4f325bcb753931d33c505142ad0728386
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 09:46:44 -0700
Commit message:

 enhancerHomologSearch 1.15.2: Replace GenomeInfoDb with Seqinfo in Imports
Package: dominatR
Commit: 288df7a095b78204ba950d086e34ecf482845170
Author: slizarazo21 <simonl3@illinois.edu>
Date: 2025-10-22 11:41:29 -0500
Commit message:

 Bump 0.99.3 complying with the review comments, changes in function redundancy, changes in documentation, and more
Package: dominatR
Commit: c6e44bdc9f6746f17ad90e2f48fd7e610e5d65a8
Author: 13rajendra <130776338+13rajendra@users.noreply.github.com>
Date: 2025-09-23 11:42:29 -0500
Commit message:

 Update README.md
Package: DspikeIn
Commit: 3403bbda60516dcb54cba4a61dd3488bdb2e1dd3
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 18:40:16 +0200
Commit message:

 Bump version to 0.99.25 for Bioconductor rebuild
Package: DspikeIn
Commit: 60732757fe8bd97fc0ab40561e6a134e187a9a0d
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 18:25:31 +0200
Commit message:

 Restore full package structure and all source files
Package: DspikeIn
Commit: 89b30a12e22dd4362b29bae79c5793a12b0bf945
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 15:56:35 +0200
Commit message:

 Reduce vignette runtime and subset data for Bioc build
Package: dominatRData
Commit: eca9c4cc0baf0bac2ba7fed0d922f56a112a0895
Author: slizarazo21 <simonl3@illinois.edu>
Date: 2025-10-22 11:32:24 -0500
Commit message:

 Modifications for bump 0.99.1, changes in description, news, vignette
Package: dominatRData
Commit: 9928c4fc09b27642406407408cadb59de357476d
Author: slizarazo21 <simonl3@illinois.edu>
Date: 2025-10-13 14:43:01 -0500
Commit message:

 Add NEWS.md
Package: BiocPkgTools
Commit: fe8a5c1abd52d35fdf0c31168ddc32e95c200305
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:53:06 -0400
Commit message:

 version bump 1.27.13
Package: BiocPkgTools
Commit: 532fae45d95adc769bf6b9af09c72c05a8764ca4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:54:42 -0400
Commit message:

 update NEWS
Package: BiocPkgTools
Commit: 01cc3eca5fc259f3537212467949e7bc089bc01b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:52:59 -0400
Commit message:

 add tests for biocVIEWSdb
Package: BiocPkgTools
Commit: 5af19667fee14b3731ef2ec6f64023d16bbe7dbd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:52:00 -0400
Commit message:

 check version inputs throughout
Package: BiocPkgTools
Commit: ce287a0d7351eede8af0587b4d55f2979ff92669
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:37:56 -0400
Commit message:

 cache VIEWS files URLs
Package: BiocPkgTools
Commit: 4e9138b3bae7c6d98a8e399541a303ac10450fd2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:21:11 -0400
Commit message:

 minor formatting
Package: BiocPkgTools
Commit: acec2affcc4b6a2bfa5a911fe55353f53e73ed25
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:21:01 -0400
Commit message:

 clean up docs in biocBuildReport and use param inheritance
Package: BiocPkgTools
Commit: bfa55f0d4ccacf7404fa14317c9d511cd5280338
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:20:31 -0400
Commit message:

 allow keywords in biocPkgList
Package: BiocPkgTools
Commit: 4a5555494044ac96c72eda0f0dd2ab85d3c77134
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-22 11:20:02 -0400
Commit message:

 extract and document biocVIEWSdb function
Package: GenomicRanges
Commit: 9009c9a26a194f1a5cf6a9bbfb0f1285ec735dee
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 08:26:48 -0700
Commit message:

 GenomicRanges 1.61.6: Small hack in updateObject() method for GRanges object

See R/GRanges-class.R for the details.
Package: Seqinfo
Commit: ddc0bc0152b7675f4ef6a1db8c85464fcb9fafd3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-22 08:21:23 -0700
Commit message:

 Seqinfo 0.99.3: Add update_Seqinfo_object()

Make updateObject() method for Seqinfo objects available as regular
(non-exported) function update_Seqinfo_object().
See IMPORTANT NOTE in R/Seqinfo-class.R for the motivation behind this.
Package: leapR
Commit: 4ff3d3855e408e53ab07657c2c558b3c6e8cada6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-14 11:27:32 -0700
Commit message:

 Fixed some issues exposed in spammR
Package: leapR
Commit: 0f07ed400a3649457985638e53245a040347e9f4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-13 19:17:52 -0700
Commit message:

 forgot to remove TODO items that were done
Package: leapR
Commit: 03b09776b48ae49a867ab0bdf493e277c86d6d77
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-13 18:18:03 -0700
Commit message:

 removed msigdb
Package: leapR
Commit: 9711e33bf209ed0905f127697583952a52e647c6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-13 17:25:09 -0700
Commit message:

 fixed errors and warnings
Package: leapR
Commit: 842ab0f0a4d8cf543a33be7b34580986f3a7b75a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-13 09:09:28 -0700
Commit message:

 added unit tests and continue to comply with bioc rules
Package: leapR
Commit: c0c5256aa71597d04d454828a88291b5b721cd60
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-09 14:49:28 -0700
Commit message:

 Add NEWS.md
Package: leapR
Commit: 19d6bfbe6780365e2e08ecf789a89c610fd3b56e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-09 14:40:38 -0700
Commit message:

 initial commit of latest changes

Addresses some of #54
Package: UCSCRepeatMasker
Commit: a5209614df42779d63169dab35cc64e17be4f6ca
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-10-22 07:50:44 -0700
Commit message:

 Add GenomicRanges in depends
Package: tanggle
Commit: 217e91a2143d6289cb0f4bda542f3eedd8823259
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-22 16:36:54 +0200
Commit message:

 remove comparison vignette for bioconductor version
Package: tanggle
Commit: 44a7cfbeaabc0c118052a14f21fd6f170051ad26
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-22 16:30:13 +0200
Commit message:

 remove now ignored directories ms and tmp
Package: tanggle
Commit: f94d1dd766ca4e8627f5f8fc60bf349376af5e9a
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-22 15:06:39 +0200
Commit message:

 bug note
Package: tanggle
Commit: 21d835620fbd51cc4b5a04461d4305f43008a4e3
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-22 14:53:30 +0200
Commit message:

 increase version number for bioconductor
Package: tanggle
Commit: 6a8be19b2cd194154aaa76491ad5e143d72e4a28
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-22 09:08:49 +0200
Commit message:

 nicer formating
Package: tanggle
Commit: 75fe6b9c210f818921993ed5513a5340d3a14d31
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-21 15:04:58 +0200
Commit message:

 fix aspect ratio in ggsplitnet
Package: tanggle
Commit: 3dbe0e6b098f6b4fc901f531836647f4093f975e
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-20 16:44:05 +0200
Commit message:

 add nymania example
Package: tanggle
Commit: fe6dd20fbef6ff1543daa6562a00df05a4ee591e
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-20 16:22:45 +0200
Commit message:

 add nymania data set and example
Package: tanggle
Commit: b80bfe355453b568cad9d90cb39530ed35850c51
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-20 15:52:18 +0200
Commit message:

 add Nymania data
Package: tanggle
Commit: 72891cdd451ef0458d707d00131d61d271afb86e
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-17 16:40:17 +0200
Commit message:

 test if files get ignored
Package: tanggle
Commit: e235ebf31cd6b0ed3518cbab0b9e11a8026061a1
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-17 16:07:55 +0200
Commit message:

 prepare for changes in ggplot2 and ggtree.
Package: tanggle
Commit: 02f56e28bacac8aea3c90ff6b439a2cf167c9d5c
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-10-17 10:27:08 +0200
Commit message:

 Merge pull request #13 from crsl4/master

Added benchmark comparison to ggret
Package: tanggle
Commit: b8b1488f40b75cfa726ef26b809d3217ff43ece0
Author: ClaudiaSL <solislemus@wisc.edu>
Date: 2025-10-16 10:38:11 -0500
Commit message:

 Merge branch 'master' of https://github.com/KlausVigo/tanggle
Package: tanggle
Commit: e273e06ebf8a294d660498c71033f43bfd3728dc
Author: ClaudiaSL <solislemus@wisc.edu>
Date: 2025-10-16 10:37:13 -0500
Commit message:

 added benchmark with ggret, code by Luis Francisco Henao Diaz
Package: tanggle
Commit: 003b0713c51e492e425b306ca585f60e1f377e7f
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 16:29:21 +0200
Commit message:

 bugfix
Package: tanggle
Commit: db324526af3c544364dd08556739887478c85331
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 16:15:01 +0200
Commit message:

 small improvements
Package: tanggle
Commit: 6ac926b96faf1cdad23feeadfbf38e8305bff6b0
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 15:52:21 +0200
Commit message:

 change logo folder
Package: tanggle
Commit: c031da54a36829ea07eed3d4cf12caf756c72510
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 15:17:55 +0200
Commit message:

 bugfix
Package: tanggle
Commit: 5264f9b86160be1e83d5b923f11f9648975d9d4e
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 15:16:42 +0200
Commit message:

 use Biocthis badges
Package: tanggle
Commit: 88a255a0a3178a1383293bee0d0d2a28734e6982
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 12:54:15 +0200
Commit message:

 try updating pgkdown
Package: tanggle
Commit: 2b3a508ceac4e79e14d5c34d29fe73a00a04d645
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 11:48:55 +0200
Commit message:

 and add man page with new references
Package: tanggle
Commit: df2baeeaf64ce8e664e5fd933e78a30a7c2de7c0
Author: Klaus Schliep <klaus.schliep@gmail.com>
Date: 2025-07-11 11:46:27 +0200
Commit message:

 add citations
Package: tanggle
Commit: 4760d33c09c91ff581a49f039bc4601a36c6ad3b
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-05-30 14:50:57 -0400
Commit message:

 added write net function
Package: tanggle
Commit: 1d1b9db8a81a6eed6c3a99aa3b577918254ee2c0
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-05-30 14:48:40 -0400
Commit message:

 added script to simulate networks
Package: tanggle
Commit: 757a00595cb1884a58a2d5834e63d618fe3255cb
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-05-30 14:32:45 -0400
Commit message:

 Merge branch 'master' of https://github.com/KlausVigo/tanggle
Package: tanggle
Commit: b2127faed000aa120d1e2d3031e8d7629a22df51
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-04-12 10:44:12 -0500
Commit message:

 added everything on the current overleaf doc
Package: tanggle
Commit: 06f63955c56986e9d54836cdcc75a5ea65bf6adf
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-04-12 09:30:03 -0500
Commit message:

 removed quotes for references
Package: tanggle
Commit: 0646addb6757434d0ace5b48ecc4e074042a435b
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-04-12 09:17:58 -0500
Commit message:

 fixed title
Package: tanggle
Commit: d06d740800e755b7e938c56807d138a01c66b47b
Author: ClaudiaSL <claudiasl@mac-laptop>
Date: 2022-04-12 09:15:29 -0500
Commit message:

 started ms for joss
Package: motifTestR
Commit: dac574d504ec4662e6e014649261036a68349a89
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-22 23:55:18 +1030
Commit message:

 Version bump after adding new model
Package: motifTestR
Commit: ff967a8244775797f53230af74b3e0db229dc479
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-22 23:49:21 +1030
Commit message:

 Added GLM Poisson model
Package: motifTestR
Commit: 6d9355c164d103a39805634131538dfd5cdcc659
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-06 01:37:41 +1030
Commit message:

 Version bump after minor tweaks
Package: motifTestR
Commit: 3476b982e1401692aa938c7751e02b972fede612
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-06 01:37:11 +1030
Commit message:

 Minor speed up for all matches
Package: motifTestR
Commit: 038beece6e42bb469469fdc6e15f83c91f8b5d5f
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-06 00:26:58 +1030
Commit message:

 Minor speed up to countPwmMatches
Package: motifTestR
Commit: babac823408976a97c4a7773fac69b872809aaa7
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-03 22:47:50 +0930
Commit message:

 version bump
Package: motifTestR
Commit: 4978064acde33027a35fdfd57961e506e2c44c77
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-03 22:47:19 +0930
Commit message:

 Restored Upset plots
Package: mitology
Commit: 35135895dca25431bbeeebaa865f53472d5308b9
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-22 15:59:54 +0200
Commit message:

 resize data
Package: QFeatures
Commit: 32ca21f594b91dd41520ac7d3fb00007b94304ea
Author: Christophe Vanderaa <43441105+cvanderaa@users.noreply.github.com>
Date: 2025-10-22 14:57:34 +0200
Commit message:

 Merge pull request #251 from cvanderaa/master

Prepared the package for new Biocoductor version
Package: QFeatures
Commit: d7d0041d61bf6754a6024a936193f4bb2a74a46e
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:54:27 +0200
Commit message:

 fix: typo in pkgdown workflow
Package: QFeatures
Commit: 1234b1a4ab1241453e92e421d9b040a604c2b801
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:29:09 +0200
Commit message:

 Added missing topics to pkgdown
Package: QFeatures
Commit: bf3801773b39794a5ea07aa8ab3abee8819ccb0c
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:11:14 +0200
Commit message:

 Version bumped
Package: QFeatures
Commit: 3784a5298ebe3f8da9e36a027b95d06de64a260a
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:10:45 +0200
Commit message:

 Updated Léopold's email
Package: QFeatures
Commit: cf82bbf8fcd09659688945991b6ec8282f83e750
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:10:16 +0200
Commit message:

 docs: added contribution section in README
Package: QFeatures
Commit: 4e1e5f38e7d57090753ab8f4538c53f082de45fa
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:09:39 +0200
Commit message:

 Updated NEWS
Package: QFeatures
Commit: 1b44896e5bf6c8a8ff0c2c223f800beb756af840
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 13:06:55 +0200
Commit message:

 fix: 'healed' some merging scars
Package: QFeatures
Commit: 234527c2a8c9807c127e5e6d02a998da1aebbe4f
Author: Christophe Vanderaa <43441105+cvanderaa@users.noreply.github.com>
Date: 2025-10-22 12:50:13 +0200
Commit message:

 Merge pull request #223 from rformassspectrometry/uniquePrecId

Create unique precursor ids and use them in joinAssays()
Package: QFeatures
Commit: 897506bf0cb90105288453d6627daa343e4aef85
Author: Christophe Vanderaa <43441105+cvanderaa@users.noreply.github.com>
Date: 2025-10-22 09:46:09 +0200
Commit message:

 Merge pull request #250 from cvanderaa/uniquePrecId

Fix Unique prec
Package: QFeatures
Commit: c4e05c456a3a8e8edc95ebec6118d75825a51021
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-22 09:44:15 +0200
Commit message:

 fix: fixed some unit tests
Package: QFeatures
Commit: 1716934a433d6912b0592c98d5fda1a07279502d
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-21 17:05:36 +0200
Commit message:

 Merge branch 'master' into uniquePrecId
Package: QFeatures
Commit: db49014c4a63da79a5fdd1086ad770fdaeafc6f2
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-21 17:05:18 +0200
Commit message:

 Merge branch 'master' of https://github.com/rformassspectrometry/QFeatures
Package: QFeatures
Commit: 426ad91af9ad0ebb2b94c345d92f4f53b210183e
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-10-21 17:05:09 +0200
Commit message:

 fix: fixed some unit tests
Package: QFeatures
Commit: a1488d0dadda668b141b1879b9216be7e53ef23f
Author: Christophe Vanderaa <43441105+cvanderaa@users.noreply.github.com>
Date: 2025-10-21 16:53:43 +0200
Commit message:

 Merge pull request #234 from alyst/respect_quant_cols

readQFeatures(): don't ignore colData$quantCols
Package: QFeatures
Commit: 0e1eb3377a1458c0a44bf60a58950f42d4fd2943
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-10-21 12:22:46 +0200
Commit message:

 Merge pull request #247 from cvanderaa/uniquePrecId

Fixed joinAssays with fcol so that assayLinks are correctly created
Package: QFeatures
Commit: dfcf14d17b9610026e56b22579b44c0c34d5975d
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-09-30 12:56:38 +0200
Commit message:

 test: fixed some unit tests
Package: QFeatures
Commit: 40faad6f07446943bd389a15fe32f68fdcc64cf3
Author: Alexey Stukalov <astukalol@seer.bio>
Date: 2025-10-03 11:53:02 -0700
Commit message:

 fix: made unique sample identifiers in multi-set multi-quant case
Package: QFeatures
Commit: 57010cf2bc4cef9e2e72cd22d0ffeaf9235272c4
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-07-02 13:16:18 +0200
Commit message:

 fix: fixed fnames when reading QFeatures and added unit tests
Package: QFeatures
Commit: 8e9113f3813a31ac65b371771b6fff561f294732
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-07-02 10:46:06 +0200
Commit message:

 fix - fix small bug
Package: QFeatures
Commit: 3425ca39bcc519f51c32761c47a935cc9a115096
Author: Alexey Stukalov <astukalol@seer.bio>
Date: 2025-06-21 15:26:51 -0700
Commit message:

 .formatColData(): simplify

remove quantCols argument since it is not used,
and the rownames should be derived from colData$quantCols and colData$runCol
Package: QFeatures
Commit: 42006ee526923cb8ce0066294380edbf5e5ae307
Author: Alexey Stukalov <astukalol@seer.bio>
Date: 2025-05-19 12:34:37 -0700
Commit message:

 readQFeatures(): test shuffled colData
Package: QFeatures
Commit: 325e04a1f39b5eedaf9a684a690cfc24c01862ef
Author: Alexey Stukalov <astukalol@seer.bio>
Date: 2025-05-19 12:34:11 -0700
Commit message:

 .formatColData: clarify rownames logic
Package: QFeatures
Commit: b8a51aed6b8aa2b19e7968feee2cb1a3cb5787f8
Author: Alexey Stukalov <astukalol@seer.bio>
Date: 2025-04-23 13:50:14 -0700
Commit message:

 .formatColData(): take $quantCols into account
Package: QFeatures
Commit: aab02fc485d7725d20f5d8455ed9306207b28226
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-06-17 12:42:30 +0200
Commit message:

 [FIX] - joinAssays allows for fcol and automatically generates the assayLinks
Package: QFeatures
Commit: b27b0335d8e836e105a3acbe528e1842bd59a06d
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-06-17 10:30:58 +0200
Commit message:

 Solved conflicts with master
Package: QFeatures
Commit: ac498f9f4d1fcff3854604fce639ad45c18b7133
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-06-17 10:22:36 +0200
Commit message:

 Merge branch 'master' of https://github.com/rformassspectrometry/QFeatures
Package: QFeatures
Commit: 71a2ff822a767b0546673eae508b8f17b849f75c
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2025-05-16 17:35:43 +0200
Commit message:

 merged upstream master
Package: QFeatures
Commit: dc265cc39bb7cc27b53f7d1559c7bde544d9ea24
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-25 08:57:42 +0100
Commit message:

 fix and notes
Package: QFeatures
Commit: d4ab105ac31fd2b6b8e063b09f979aea3cb43161
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-24 10:04:30 +0100
Commit message:

 remove benchmarking code
Package: QFeatures
Commit: 598d30fafa3cc93d1e56034e7cc50053a8220646
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-24 09:38:00 +0100
Commit message:

 testing a .setAssayRownames() with an i
Package: QFeatures
Commit: dd777db24526208d07e36cd864c7de55fb98c74e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-24 06:22:38 +0100
Commit message:

 udpate man page
Package: QFeatures
Commit: dc577a3d23fc9a73c373a92feb74fea8e14b7880
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-23 22:49:13 +0100
Commit message:

 fix warnings and update api
Package: QFeatures
Commit: abe0eec9cdf21e12db5cd0480d8d794d624dd3b5
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-23 22:09:38 +0100
Commit message:

 create prec ids and use in joinAssays()
Package: QFeatures
Commit: 92e0306995b7ae25e2b6c0982e34b1cfa0608d97
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-23 17:53:13 +0100
Commit message:

 Merge branch 'master' into uniquePrecId
Package: QFeatures
Commit: fe805882771c05ed5156f1fd69b9c6fc47e4bbc6
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-02-08 16:30:30 +0100
Commit message:

 new createPrecursorId function
Package: QFeatures
Commit: 6a3357c78ee25da4c84f210bf10c2f5e495e8faa
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-12-18 17:27:52 +0100
Commit message:

 synced with upstream's master
Package: QFeatures
Commit: 49f5be5b188a41c1864cbc3cbdd6d2d97816a00c
Author: cvanderaa <vanderaa.christophe@gmail.com>
Date: 2024-12-18 17:25:51 +0100
Commit message:

 Revert "fix: solved  bug and adapted unit tests"

This reverts commit f89825fb545aa111964aff1ff16d4c3e54159268.
Package: Rarr
Commit: 2a26f91c032f8135c35d801b218e36baf8fdb3ba
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-22 15:29:07 +0200
Commit message:

 Mention call counting in NEWS
Package: Rarr
Commit: fa091b537ad78ce2be87a1688196c48819ea4c39
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-22 15:26:08 +0200
Commit message:

 Bump version
Package: Rarr
Commit: 76343ea39ea045c1c69eaf08ced299faa93b3826
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-22 15:23:21 +0200
Commit message:

 Add test to count function calls
Package: Rarr
Commit: 9535386d5663fe7068bae6e74faf1c94b8e95be4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 13:15:39 +0200
Commit message:

 Split for loops in tests
Package: Rarr
Commit: 7f4aca4aedfb59ae498ac2c9c845b8a88e015e01
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-16 09:14:09 +0000
Commit message:

 Remove type condition for touchstone trigger
Package: Rarr
Commit: 05b48f44b9e4a2a02ffd13014843a11f546ac741
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-16 10:04:40 +0200
Commit message:

 Run devtools::document()
Package: Rarr
Commit: 12ec507c2a2b15cdabf3cd7c425435ca75a5ba5d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 23:23:04 +0200
Commit message:

 Add benchmarks for reading/writing basic types
Package: Rarr
Commit: 0d0d59a641b96a24d010d20cf98dc37d4bc38285
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 10:30:14 +0200
Commit message:

 Move withr to Suggests
Package: Rarr
Commit: 7237747b17fbe75f8aa5d28a82e29e6d4b40aa88
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 08:57:49 +0200
Commit message:

 Create s390 (big endian) GHA workflow

Based on https://gaborcsardi.org/2024/gha-s390x/
Package: Rarr
Commit: e22d191a835171dc524829b7999c98674a84e55a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-15 10:27:47 +0200
Commit message:

 Import stats::setNames() explicitly
Package: DspikeIn
Commit: 4e80230529cea44fa7d262dd4573c1e29ba34b4d
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 15:22:53 +0200
Commit message:

 Update README with Bioconductor and GitHub installation instructions
Package: DspikeIn
Commit: b8f26e9e1dd0e5f56e3ccf2a7ddf94fd3f6e3964
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 15:05:59 +0200
Commit message:

 Resolve README merge conflict after merging devel
Package: DspikeIn
Commit: a78606522487f8bb56eb9dae5e4a71845b5234ac
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 15:04:05 +0200
Commit message:

 Update DESCRIPTION and NEWS before merging devel
Package: DspikeIn
Commit: 90581bf6b90bb912bdf0a5bc104b0b5a7977d941
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:58:38 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: eb5d039cd1a97dde5a1db1d1f342ff10edf756c0
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:55:14 +0200
Commit message:

 Cleaned remaining merge markers
Package: DspikeIn
Commit: da4103dcc231dd2fa1f413b71659b560fc16c2ad
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:47:52 +0200
Commit message:

 Remove leftover merge conflict markers
Package: DspikeIn
Commit: 909e362999f156f09e93fc156d4d9d3d34882d91
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:41:58 +0200
Commit message:

 Bump version to 0.99.22 and update NEWS for Bioconductor rebuild
Package: DspikeIn
Commit: 562363bc2bcd9fc67e92b03ca1869f9b071e9268
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:22:25 +0200
Commit message:

 Resolved merge conflict markers after bioc-rev1 merge
Package: DspikeIn
Commit: cbdf88c65ec4607d9d9f4bd18135f416eafb7319
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:16:01 +0200
Commit message:

 Merged bioc-rev1 into devel for Bioconductor resubmission (0.99.21)
Package: DspikeIn
Commit: dd3b6d2b5fd1f3fb3dc1434ae55843c76a13db6f
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-10-22 14:06:59 +0200
Commit message:

 git checkout --ours README.md
git add README.md
git rebase --continue
Final local edits before Bioconductor merge (0.99.21)

git checkout --ours README.md
git add README.md
git rebase --continue
q1
Package: DspikeIn
Commit: 24ef7db71297f3e688eca64643710a11c6e0a524
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-10-05 11:22:47 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 961c61a272a4955346acd429a145189d71a5c441
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-15 14:00:05 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: b1fd0e6bd0278d3ec0c382fa22cd77638994c45d
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-13 15:24:37 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: cdc8d279aa65519d08dcd930dbc2fa4fa818a137
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-13 13:14:59 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 163be4c78752cb1975516f066712551870907c34
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-13 13:13:18 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: de9189f7c7af2a1521e38dc50b2beb9e2e40a854
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-13 13:10:54 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: dcef2c217df0d75679772faead31c6aa4c9927c2
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-13 13:08:49 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 4b9024bc5f88f444feb65beb0a56a64082cbb5fb
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-08-13 13:02:53 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: b49feb95dd6a814c6a4e5b5c9df687440993d92b
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-07-21 22:41:46 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 25cb5f926555235326bf5a653c0dfbdb04327763
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-07-21 22:37:55 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 9a5bcbbcf666516ae16e0eb6b5069dffaf7db710
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-07-21 22:37:08 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 29a985fae98cd604dcbbf4b66edf73d5a3d083d8
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-07-21 22:36:21 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 3fa0fe3547eb7fd908b95a71b06e9256b54ee6a2
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-07-21 22:34:57 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 30ed17072fed1b2894afdba0dd042350f409c748
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-07-21 22:26:01 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: ed53143556a14d0f00ae41e63daedd5a7ad1e13f
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-23 16:04:02 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 37ab98c4d1631a88411defaf1256cdab245568bb
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-23 13:40:58 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: b86deb0e006d128e0f59a42ef543cd8c49c42b39
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-23 13:32:56 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: e26596d961f3f15bdfb6e183a723c4b93fbe860d
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-20 20:14:33 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 3f49ddc91b5300ce47873213a1195bcb0ac56320
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-20 19:29:49 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 6ae47e7bbb7ee4250c8899f2119305077ed5b288
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-20 19:24:27 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: fa47934ad396c768785e6bf9f3461ab6473c5e3d
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 19:06:50 +0200
Commit message:

 Move vignettes to root-level docs folder for GitHub Pages
Package: DspikeIn
Commit: 003d1510b6e911f250511b93afe648793607b9ca
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:57:34 +0200
Commit message:

 Remove .DS_Store from tracked files
Package: DspikeIn
Commit: a73aba0c26f4c25efe111a93af4af40aa103a559
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:56:33 +0200
Commit message:

 Remove placeholder file from R/ folder
Package: DspikeIn
Commit: 693faccef59c625bb8fad9e7f9f234921b68ae46
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:55:10 +0200
Commit message:

 Add .DS_Store to .gitignore
Package: DspikeIn
Commit: 020607b1181c5617693148b6c537fabb096f2447
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:53:57 +0200
Commit message:

 Force update: refresh timestamps of R/ scripts
Package: DspikeIn
Commit: 93cd0c2ab492848afe740517dae631be8ad86223
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:46:27 +0200
Commit message:

 Cleanup: remove R/.placeholder
Package: DspikeIn
Commit: 972766e918fd8d9ee67da228bd701167cd45a7c6
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:45:57 +0200
Commit message:

 Force update: ensure R/ folder and scripts are tracked
Package: DspikeIn
Commit: 0047506acfcadf36ce00f290f5052cb2bc1cf4c1
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 18:38:42 +0200
Commit message:

 Remove .DS_Store and add to .gitignore
Package: DspikeIn
Commit: bd34c7794bda2d930ec4ac6e01dda32738669fc8
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 17:55:47 +0200
Commit message:

 Manual commit: update vignettes and docs to MGhotbi
Package: DspikeIn
Commit: 63a4ed097472e532b3393b9eb081581312c91a32
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 17:00:58 +0200
Commit message:

 Re-ignore docs/ folder
Package: DspikeIn
Commit: f2c05e2fe411cd99ac6eeefee1c549656d01d7e5
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-20 15:55:57 +0200
Commit message:

 adding TSE examples
Package: DspikeIn
Commit: 3fbc250a5d1a35f09a2e3a04a90d2f4b13069b7f
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-18 17:54:05 +0200
Commit message:

 Merge MGhotbi: resolved README.md conflict
Package: DspikeIn
Commit: 33b0731e0bc045dd7e3cd093dd01834a9147112e
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-18 17:46:47 +0200
Commit message:

 Complete Bioconductor update: refine vignettes, restructure data, update DESCRIPTION and Rd files, remove outdated content
Package: DspikeIn
Commit: 95e67214fa8a2e91d4ab02169c59c2f238d725b8
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-02 09:27:07 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 79dae8b8496c892a6982bec804db1dcfca07466c
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-02 09:25:30 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: e96ef0ad2db9fa540b8710a0f79e14a7ae77a7a8
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-02 09:24:11 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: ea7b3a94a798a48ab7eef0e402de5b5f78d2cdb2
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-02 09:22:21 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 38b2f0e24340a5b2238177d634d4f8b47852048e
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-02 09:21:06 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 94dbbafb75ef86b65a9fbca387a0581475645174
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-02 09:20:32 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 3848751b95c919d0ded0341de634c83eda6ec018
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-01 11:11:02 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 9f3af87b0f76db8c369eeb35da32788e5e4165e8
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-01 11:10:22 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: f9af4aa7dc3f1eec77be8a17b503f884342578a2
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-01 11:09:48 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: bca083c23d99fb05ab84f8dfc063173884ea625d
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-01 10:03:13 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: 9451671f3ae5d73832a590be00f50fd0c05be4c2
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-01 09:24:31 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: a687f823bdfb6f9fa6a32bd6d95a518e5f09615b
Author: Mitra <mitra.ghotbi@gmail.com>
Date: 2025-06-01 09:19:12 +0200
Commit message:

 Update README.md
Package: DspikeIn
Commit: e3503796167c2a94b09264431e99f1d91692e438
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-01 09:14:29 +0200
Commit message:

 Add PDF vignette to GitHub Pages
Package: DspikeIn
Commit: 2b3874b263e2b75021bb0269b216372c50ab9f54
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-01 09:04:31 +0200
Commit message:

 Add index.html for GitHub Pages
Package: DspikeIn
Commit: 2d141cbfa2691393440318db467257cc55ba497b
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-06-01 08:50:28 +0200
Commit message:

 Add index.html for GitHub Pages
Package: DspikeIn
Commit: 3a822aaeb42d4932e482a527b4b91cc7c7d5fcb2
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-05-31 22:54:51 +0200
Commit message:

 Add GitHub Pages HTML vignette
Package: DspikeIn
Commit: 01bdb04f9a5238f62cfd9c3ac7cf66cf3c0c3bd9
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-05-31 22:16:16 +0200
Commit message:

 Remove rendered HTML vignette
Package: DspikeIn
Commit: 0f3409259c2d6ed0259fd5024fed0464598175e2
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-05-31 22:12:38 +0200
Commit message:

 Add rendered HTML vignette
Package: DspikeIn
Commit: 2fdb1dbe0f2e4a82e418c741803531a80864f526
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-05-31 18:37:33 +0200
Commit message:

 Restore full pipeline after accidental overwrite
Package: DspikeIn
Commit: f385da46f8d9c6131486141953e0a992c0137b0c
Author: Mitra Ghotbi <mitra.ghotbi@gmail.com>
Date: 2025-05-30 22:08:18 +0200
Commit message:

 Full pipeline for lab - MGhotbi branch
Package: MetaboDynamics
Commit: fabf07fa129e46b25de38e0365baf8bcd552e198
Author: Katja Danielzik <katja.danielzik@stud.uni-due.de>
Date: 2025-10-22 14:32:36 +0200
Commit message:

 vignette and news polishing
Package: MetaboDynamics
Commit: e47b5539ce784d73ef29c51ee0a0005079b4dd1f
Author: Katja Danielzik <katja.danielzik@stud.uni-due.de>
Date: 2025-10-22 12:54:56 +0200
Commit message:

 Merge branch 'devel' of github.com:KatjaDanielzik/MetaboDynamics into devel
Package: MetaboDynamics
Commit: 1c736f737973205631c26275770c5e626c0ef9ae
Author: Katja Danielzik <katja.danielzik@stud.uni-due.de>
Date: 2025-10-22 12:54:52 +0200
Commit message:

 typos
Package: mCSEAdata
Commit: e7fd1eb1f83e279ad3105762bd5cacfdb8cb0d64
Author: jordimartorell <jmartorellm@gmail.com>
Date: 2025-10-22 12:44:33 +0200
Commit message:

 Add EPICv2 support
Package: scDblFinder
Commit: 86b90b4a49d9afca3cc28187979af26fddac696b
Author: plger <pl.germain@gmail.com>
Date: 2025-10-22 10:51:33 +0200
Commit message:

 updated namespace
Package: scDblFinder
Commit: ebacdcfd147df2f9c83fce713bee9d787aeb4438
Author: plger <pl.germain@gmail.com>
Date: 2025-10-22 10:46:27 +0200
Commit message:

 version bump
Package: scDblFinder
Commit: 917e420f68ec674a14ece8781e0f7f03ce8e61cb
Author: plger <pl.germain@gmail.com>
Date: 2025-10-22 10:46:10 +0200
Commit message:

 import xgb.DMatrix for all xgb versions
Package: scDblFinder
Commit: 207b27e437d2ac750363cd97ce8f6a672ee2d660
Author: plger <pl.germain@gmail.com>
Date: 2025-10-22 10:39:13 +0200
Commit message:

 added xgboost imports conditional on version
Package: Chromatograms
Commit: f3e2cd780ccccf4f8a4b3d7c289ca0d9ba66c1f0
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2025-10-22 10:23:32 +0200
Commit message:

 Merge pull request #43 from rformassspectrometry/phili

Implement chromExtract and imputePeaksData
Package: Chromatograms
Commit: de8d302555f3cf31a0b7dedd9693807ac3ce8cc8
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-10-22 09:15:12 +0200
Commit message:

 fix docu and simplify factorisation for Spectra backend.
Package: Chromatograms
Commit: 3265244e9a54ba2f806b20ca0fce07d28c2d70fb
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-10-14 17:18:11 +0200
Commit message:

 feat: mapping spectraVariables.
Package: Chromatograms
Commit: b6606ad2e7da6c87b955041718f4eb69fc0dbfcf
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-10-14 14:16:15 +0200
Commit message:

 add lengths() and complete coverage
Package: Chromatograms
Commit: c7310f532681ae6f89ee2d25f57df894c29aec15
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-10-14 12:52:26 +0200
Commit message:

 feat: chromExtract() and imputePeaksData
Package: Chromatograms
Commit: d1b351248392179a8a444eeb6604c48e86aaebe5
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-10-06 10:42:54 +0200
Commit message:

 Merge branch 'main' into phili
Package: Chromatograms
Commit: 3fe7ffdc5fa1ba0484836c32fa51bbc6a41c1187
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-09-24 11:18:47 +0200
Commit message:

 first round of fixes
Package: notameViz
Commit: 47f9fcbdab3489152dbed30bd9ccf2cf4b269312
Author: attlih <98050742+attlih@users.noreply.github.com>
Date: 2025-10-20 10:10:48 +0300
Commit message:

 Change deprecated  argument in ggplot
Package: notameViz
Commit: f29bf7e462c78f810a358394bc5d98d586b141aa
Author: attlih <98050742+attlih@users.noreply.github.com>
Date: 2025-10-20 09:59:53 +0300
Commit message:

 Version bump
Package: notameViz
Commit: 07a4203a21f2ae7d70999a91c5793e4b4c08262e
Author: attlih <98050742+attlih@users.noreply.github.com>
Date: 2025-10-20 09:39:11 +0300
Commit message:

 Quality flag barplot should be generated with all features
Package: notame
Commit: 1a02e4b140d38780c3fb2867e4ffe374221dff81
Author: Retu Haikonen <93867575+RetuWonData@users.noreply.github.com>
Date: 2025-10-17 12:02:35 +0300
Commit message:

 Update flag_contaminants (#13)

* Updated flag_contaminants to also handle mean and max

* Corrections to code and documentation based on pull request review.

* Adjusting the blank_type default accordingly.

* Correcting the default threshold.

* Update example to correspond to default arguments

* Version bump

---------

Co-authored-by: vsuksi <vsuksi@abo.fi>
Co-authored-by: vsuksi <104491648+vsuksi@users.noreply.github.com>
Package: notame
Commit: 0090e665d8445e822b3ce10e38dde62f30803726
Author: vsuksi <104491648+vsuksi@users.noreply.github.com>
Date: 2025-10-17 11:51:44 +0300
Commit message:

 Create website AND perform checks (#15)

* Change check options

as_cran = false to "resolve" warning I'm not getting with standard flags 
(no mention in Bioc documentation that --as-cran flags should be used).

* Testing behavior of rworkflows (#14)

* Small index change (to test if website updates from PR)

* Cleaning

* One-liner to build and deploy site only on push to main branch
Package: CSOA
Commit: e6c667842b8b0887017066dee727e556f9e0ebe2
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-10-22 14:13:23 +0800
Commit message:

 Reduced direct dependencies
Package: GenomicFeatures
Commit: 86cef6ec6e7d8c72be0c7508e987650a6166bbc7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 22:31:40 -0700
Commit message:

 GenomicFeatures 1.61.7: Repair unit tests

New TxDb.Hsapiens.UCSC.hg19.knownGene (version 3.22.1) broke some of the
unit tests in inst/unitTests/test_select-methods.R
Package: fastreeR
Commit: cc4fa7d80c9d6c29455ec8173a111f8a87caa4e5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 04:33:17 +0200
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 40f009e4c35d871ee2154c303834ca982fc56b17
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 04:33:15 +0200
Commit message:

 Fix docker JRE version
Package: fastreeR
Commit: 8c9546259ab0f6876271c93f9cf7418b5d0376c5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 02:28:57 +0000
Commit message:

 Update fastreeR to version 1.99.8 with backend version 2.1.1
Package: fastreeR
Commit: f59705ba135577d775393f2d8839056cfe76aa1e
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 04:22:56 +0200
Commit message:

 Fix docker java version
Package: fastreeR
Commit: a5cac81fe70393a84d88e3d80750e3426173e1e9
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 01:55:18 +0000
Commit message:

 Update fastreeR to version 1.99.7 with backend version
Package: fastreeR
Commit: f10716f7e5b3e4711a86f32f0213ce81df163501
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 01:12:57 +0000
Commit message:

 Update fastreeR to version 1.99.6 with backend version 2.1.0
Package: fastreeR
Commit: 22305a9fce3dcba468850c6d1870304da3608008
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 03:10:39 +0200
Commit message:

 1.99.5
Package: OSTA
Commit: 339894dce2cccefee50a99cc1872d57cf253d1ce
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 22:30:34 -0400
Commit message:

 version and date
Package: OSTA
Commit: 90e48dbc2beb3bbd39a5f59ba337abb46541d187
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 22:30:06 -0400
Commit message:

 typo
Package: OSTA
Commit: ea723c8cc0d55b3e518b57e12049d5e3f6b58623
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 22:28:53 -0400
Commit message:

 Merge pull request #234 from Mengbo-Li/sandbox

Add scider section to "img-neighborhood-analysis" chapter
Package: OSTA
Commit: c0943f1044aabb3b0977b92415461e7604b63439
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 19:19:01 -0400
Commit message:

 Merge branch 'sandbox' into sandbox
Package: OSTA
Commit: d58551ade28900c66bd34de2f8134d6287c80aa3
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 19:12:29 -0400
Commit message:

 add scider references
Package: OSTA
Commit: 3f2663000b4af0d484007194787589304a95fdf5
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 19:12:21 -0400
Commit message:

 update scider code and references
Package: OSTA
Commit: 980fa7c641c3cfeadafb84ef3d35fb63277f4e0a
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 19:06:56 -0400
Commit message:

 add scider to DESCRIPTION
Package: OSTA
Commit: a83c9815ca63d9b3ce39d4c710bf2cd4b2469314
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 14:50:49 -0400
Commit message:

 Merge pull request #237 from shazanfar/sandbox

add img-sub-cellular-analysis chapter
Package: OSTA
Commit: 7981c7f932be534c342f5713adef0f8c426acd67
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 14:49:09 -0400
Commit message:

 Merge branch 'sandbox' into sandbox
Package: OSTA
Commit: 765a47f4bd9d7ecdd09597618d726359adfe6527
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 08:50:14 -0400
Commit message:

 clean up
Package: OSTA
Commit: 45a99dc9b50fea2065c53f5d8167552177c7676a
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 00:19:15 -0400
Commit message:

 use numpy v1.26.4
Package: OSTA
Commit: 0d7a921149b17510b807a080b97b77ea1748e506
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-20 20:19:59 -0400
Commit message:

 re-use Python environment for CCC chapter
Package: OSTA
Commit: 13f14a141d3f7751995986b2d54bf88d378d2242
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-21 13:43:01 -0400
Commit message:

 Merge pull request #233 from HelenaLC/sandbox

+img-cell-cell-comm
Package: OSTA
Commit: 94dea703d5c341ded428b57c8f1e1e516fdabb91
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-19 18:43:05 +0200
Commit message:

 Merge pull request #236 from Artur-man/giotto_ref
Package: OSTA
Commit: ae7ef65420f2512bea340c8fd80e824837d8ea78
Author: Artur-man <artur-man@hotmail.com>
Date: 2025-10-19 18:15:11 +0200
Commit message:

 add sosta reference
Package: OSTA
Commit: 7aee3c20d365cc029685aea9ee8874d650c1ade4
Author: Artur-man <artur-man@hotmail.com>
Date: 2025-10-19 18:09:40 +0200
Commit message:

 update giotto reference
Package: OSTA
Commit: 796ad8e32891378acc7d6f9c6a20528715c6d202
Author: Pratibha Panwar <pratibhapanwar.4@gmail.com>
Date: 2025-10-17 12:58:14 +1100
Commit message:

 Added citations related to img-sub-cellular-analysis chapter in bibliography
Package: OSTA
Commit: 2720135bcce65403824867aefddf6c0acae1cd7b
Author: Pratibha Panwar <pratibhapanwar.4@gmail.com>
Date: 2025-10-17 12:57:43 +1100
Commit message:

 Added img-sub-cellular-analysis chapter to book.
Package: OSTA
Commit: 4381b8750b4f54c429b8df3f81fb7bd9e4c1e61f
Author: Pratibha Panwar <pratibhapanwar.4@gmail.com>
Date: 2025-10-17 12:57:21 +1100
Commit message:

 Added images to the img-sub-cellular-analysis chapter.
Package: OSTA
Commit: e1b4bc6907b89963d41a46a589465e0f9ebb9db3
Author: Pratibha Panwar <pratibhapanwar.4@gmail.com>
Date: 2025-10-17 12:56:51 +1100
Commit message:

 Added page for sub-cellular analysis of imaging-based SRT data.
Package: OSTA
Commit: 587b433c71b05b389d3c147ba694f5b746570a30
Author: Mengbo Li <li.me@wehi.edu.au>
Date: 2025-10-13 10:10:01 +1100
Commit message:

 Add scider section.
Package: OSTA
Commit: f11261578152972e59d5119609e9a6cb9b460629
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-10 10:15:11 +0200
Commit message:

 prettify viz
Package: OSTA
Commit: 6d376ecea8a65dd14d15e2d125207af6002f3922
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-10 09:20:49 +0200
Commit message:

 rmv old ver
Package: OSTA
Commit: 900de82874c310ef4d50a329414afed835e0cb69
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-10 09:20:03 +0200
Commit message:

 fix _book.yml formatting
Package: OSTA
Commit: 7fbfd217c320e631d0642e8ceb7f43d0f780d8f7
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-10 09:18:36 +0200
Commit message:

 hide local env definition
Package: OSTA
Commit: 8baaa925f088046a1292d323b8ef4abf53ca0f9e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-10 09:17:23 +0200
Commit message:

 add more words
Package: OSTA
Commit: c16d0584d39ac4312469cfbe725d0cd8b8c519fe
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 22:44:14 +0200
Commit message:

 +BayesSpace
Package: OSTA
Commit: d2ca3ef37ef378f7a790f36dca9c72dcc31a6c39
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 22:42:55 +0200
Commit message:

 render book completely
Package: OSTA
Commit: a5d54b07355e1aa1d157987f11b509cafc1b9f93
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 19:38:37 +0200
Commit message:

 -BayesSpace
Package: OSTA
Commit: 22d2aa7e232acb2ef561f5b99cc7136dde39d05a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 18:49:05 +0200
Commit message:

 Merge branch 'ccc' into sandbox
Package: OSTA
Commit: 212535d7e929514365d826d8bdc91d83bdae90dd
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 18:40:52 +0200
Commit message:

 skip BayesSpace (it's unavailable)
Package: OSTA
Commit: 039ffdee65a9e2bae63806b1c2c657bc6af6c435
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-09 17:50:12 +0200
Commit message:

 +img-cell-cell-comm
Package: OSTA
Commit: 62225384777471530516ab35bbb4a0c14c188ed9
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 17:49:51 +0200
Commit message:

 unchange gha
Package: OSTA
Commit: d05f244a996e257d40158ec33b670861a4372267
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 17:48:29 +0200
Commit message:

 Merge branch 'sandbox' into ccc
Package: OSTA
Commit: 4a4bf006f8fd0043f9c300095ef39703726fb5f3
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 16:39:48 +0200
Commit message:

 +Imports:CCPlotR
Package: OSTA
Commit: cb64665953049d99df02392d0da88a9081786e18
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 16:39:19 +0200
Commit message:

 +CCPlotR
Package: OSTA
Commit: b4a581635d929c1098c832a11082c85a2cdc340c
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 15:30:53 +0200
Commit message:

 use basilisk env
Package: OSTA
Commit: d6957d51fa7162377b21df472e1bcba7cf235a2c
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 15:30:37 +0200
Commit message:

 fix ref keys
Package: OSTA
Commit: 030397c5127146b3652cab3ac1d89829aa97b137
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 15:27:48 +0200
Commit message:

 add ccc refs
Package: OSTA
Commit: 0a667b2989311a0fbab1c2c1ea8e6f358819b264
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-09 15:27:34 +0200
Commit message:

 merge sandbox
Package: OSTA
Commit: c2198b617c38c07f9448637fdd6ce547951d1795
Author: HelenaLC <helena@crowell.eu>
Date: 2025-05-21 08:36:26 +0200
Commit message:

 stash
Package: OSTA
Commit: 954f51678680b805a5efea0775118efce8dd9a13
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-10 11:32:54 +0100
Commit message:

 downsize?
Package: OSTA
Commit: 4b54f89b76ac25113b0e4a521ba4b303e9d6bc4d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-10 10:31:28 +0100
Commit message:

 specify 'commot' version
Package: OSTA
Commit: 71260f1c9230713bdf768abbcc65fe7ef573700e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-10 09:02:55 +0100
Commit message:

 try explicit versions
Package: OSTA
Commit: 92d099b7da7ab6d0c11afc9079b7feea6a3bed7b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-09 21:44:51 +0100
Commit message:

 fix basilisk env
Package: OSTA
Commit: 27731465058c88118ff1badcecf881990d6ac79b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-09 18:26:24 +0100
Commit message:

 +Python dependencies
Package: OSTA
Commit: d027514767df1d43b35bd955d2148d3713409a67
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-09 17:18:51 +0100
Commit message:

 ccc test
Package: OSTA
Commit: 51402d8772afe0e354a6af043e4d0c04735dd067
Author: HelenaLC <helena@crowell.eu>
Date: 2025-02-09 17:08:08 +0100
Commit message:

 trigger GHA on PR
Package: tidySpatialExperiment
Commit: 8909c5494f1bf848ea03e4c6eff4a9a4f8e2a9b9
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-22 13:11:35 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: d1abeb67fabf3c9ad30e9249164d6f9014d257da
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-22 13:11:14 +1100
Commit message:

 Merge BioConductor repository version bumps
Package: tidySpatialExperiment
Commit: 2c6dce71e4ec53a77b8f211e562a27bcaacfac6c
Author: william-hutchison <william.8191@fastmail.com>
Date: 2025-10-10 16:13:10 +1100
Commit message:

 Merge pull request #44 from william-hutchison/fix-gate-background

Fix gate background
Package: tidySpatialExperiment
Commit: 5a05f8a071aa084183dd1cbbcb030b5c7a477cc6
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-10 15:54:47 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: ba462375b09030b7a94b2a32fffbb2cbab83d9b8
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-10 15:54:09 +1100
Commit message:

 Flip gating y axis orientation
Package: tidySpatialExperiment
Commit: be96eff9eeb53038ca9373309c8d939ecc31548a
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-10-10 15:26:12 +1100
Commit message:

 Set gate background image anchor
Package: tidySpatialExperiment
Commit: 0d67253f57eafafe88319d488fc0acf81b1d0d3e
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-09-24 14:40:39 +1000
Commit message:

 Merge pull request #41 from william-hutchison/update-gate

Update gate
Package: tidySpatialExperiment
Commit: 04b4a7b2885a7c108989b70069248385bb522105
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-09-24 14:26:30 +1000
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: b3c24da20653f803e1792afd129d2911e70d55ce
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-09-24 14:26:21 +1000
Commit message:

 Update documentation
Package: tidySpatialExperiment
Commit: 65fa446f0f22bfa1f0e6dd117d04e5fa290338dc
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-09-24 14:15:14 +1000
Commit message:

 Remove duplicated documentation
Package: tidySpatialExperiment
Commit: 685ffb537b7c96ca32994d5fa4ac9827aec40364
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-09-24 14:07:53 +1000
Commit message:

 Fix incorrect image scaling
Package: tidySpatialExperiment
Commit: d88367bd205f57ba68020f84a620b426c6c1f4ed
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-09-24 14:03:28 +1000
Commit message:

 Merge pull request #39 from william-hutchison/ECCB2024

fix gate_interactive
Package: tidySpatialExperiment
Commit: c2a8b6373a2628b76bc551593de59fd417bc15db
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2024-09-16 18:22:52 +0300
Commit message:

 fix gate_interactive for library(STexampleData) spatial_data <- Visium_mouseCoronal()
Package: SAIGEgds
Commit: bb9fa5cd901efdea1eb9afff7e5361fead8320f5
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-10-21 20:44:34 -0500
Commit message:

 attempt to fix
Package: SeqArray
Commit: 36ec555906f7e28a58628b374fcfb7e64d4cb5f1
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-10-21 20:38:55 -0500
Commit message:

 Fix ##INFO=<>
Package: SNPRelate
Commit: e5757f992f38e9c8bf29281074d2f28fde85c7b4
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-10-21 20:26:21 -0500
Commit message:

 update NEWS
Package: geomeTriD
Commit: 6dd231b6f2b4845b8a016eabad6c3237b3055a13
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-21 20:28:03 -0400
Commit message:

 improve the reset button for tjviewer
Package: epiregulon
Commit: fdde5524e8638abb4b7ca9239e15416f8cd07352
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-21 23:17:57 +0000
Commit message:

 1.99.4
Package: epiregulon
Commit: 905b68da3b5dd5dcba2e6fc998c177d7e618faa4
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-21 23:17:45 +0000
Commit message:

 fix mismatch in integer type
Package: anndataR
Commit: da283c76ce56df635ee8eb7cdd288ab978cf71aa
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-10-22 00:40:35 +0200
Commit message:

 Fix Bioc review issues (#372)

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Package: anndataR
Commit: f765aab8e4944ae7b67eab34f3bdae9982b39e03
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2025-10-17 18:02:53 +0200
Commit message:

 Add missing NEWS entry
Package: scviR
Commit: a7a94a2e5d7d3c96568655119066bf41ecb33b4d
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-21 09:30:36 -0700
Commit message:

 Merge branch 'nobas' into devel
Package: scviR
Commit: 148238d287de864d1a3f31c883261b0d40f072af
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-21 09:29:20 -0700
Commit message:

 passing check with nobas
Package: CatsCradle
Commit: 3320f14831c1f6c116b3f1b3f3eb078aeccdc0e2
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2025-10-21 22:56:09 +0100
Commit message:

 Spaces removed from description
Package: omicsGMF
Commit: 14caf2e25488f9b02293354ddff735a87ea1d534
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-21 23:03:34 +0200
Commit message:

 version bump
Package: omicsGMF
Commit: 7e32fffed52d90a616d37f4772d1bb1138bf5cf9
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-21 21:52:40 +0200
Commit message:

 minor changes
Package: igblastr
Commit: ed3b6c1dccb16d7faf06e92e52e36044d613ee39
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 12:35:57 -0700
Commit message:

 print message when the user selects a built-in AIRR germline db with .src suffix
Package: scGraphVerse
Commit: ba54489471821d43da58a8184769f1d7728f2962
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-21 20:22:51 +0200
Commit message:

 fix DESC and NEWs
Package: igblastr
Commit: 4836243ca5a3ac82054e48a18ab2bcc4acd9534c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 11:16:45 -0700
Commit message:

 oops, should have been '?list_germline_dbs' instead of '?germline_dbs_home' in previous commit message
Package: igblastr
Commit: bf159cf6108aff05a8abcd0e5a0b5d04bca2de2d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 10:55:49 -0700
Commit message:

 igblastr 0.99.23: New built-in AIRR germline dbs for human

Replace built-in germline db _AIRR.human.IGH+IGK+IGL.202501 with the
following dbs:

    _AIRR.human.IGH+IGK+IGL.202309
    _AIRR.human.IGH+IGK+IGL.202309.src
    _AIRR.human.IGH+IGK+IGL.202410
    _AIRR.human.IGH+IGK+IGL.202410.src

See https://github.com/HyrienLab/igblastr/tree/devel/inst/extdata/germline_sequ>
and https://github.com/HyrienLab/igblastr/tree/devel/inst/extdata/germline_sequ>
for how these dbs were made.

Note that _AIRR.human.IGH+IGK+IGL.202410.src is exactly the same
as _AIRR.human.IGH+IGK+IGL.202501, only the name is different. The
new name is the result of a revisited naming scheme for the built-in
AIRR germline dbs for human.
See the Value section in '?germline_dbs_home' for more information.
Package: scDblFinder
Commit: 227116a0fe7378a0679f3a5137de2fd6445c75c2
Author: plger <pl.germain@gmail.com>
Date: 2025-10-21 18:06:14 +0200
Commit message:

 version bump
Package: scDblFinder
Commit: 2bbcbf43e1bd7dc5732152be5c2cd6c4b8e7514b
Author: plger <pl.germain@gmail.com>
Date: 2025-10-21 18:05:37 +0200
Commit message:

 verbos arg name to match different xgboost versions
Package: rhinotypeR
Commit: cd2e13f84c2d847d882fb634831f8c9db99ffd00
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-21 17:08:48 +0100
Commit message:

 Merge branch 'main' of https://github.com/omicscodeathon/rhinotypeR
Package: rhinotypeR
Commit: 38a78893d0e2757f4bfc10d1836138d436902011
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-21 16:55:09 +0100
Commit message:

 solved check errors
Package: rhinotypeR
Commit: 9a149ec6819cf901908b979b321534ba60297685
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2025-10-05 15:05:08 +0100
Commit message:

 Merge pull request #10 from omicscodeathon/git-devel

ms revisions
Package: rhinotypeR
Commit: ba339370eea09c7954551ba84d4f74e92a33a4f9
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-05 15:04:05 +0100
Commit message:

 ms revisions
Package: rhinotypeR
Commit: 8b164451e15bda19a4bafc6829ebd59300f64b30
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2025-10-01 19:06:17 +0100
Commit message:

 Delete rhinotypeR.BiocCheck directory
Package: rhinotypeR
Commit: 41199a585753827e0be3be2068a1cff7ae0488a9
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-01 19:04:39 +0100
Commit message:

 manuscript revisions
Package: rhinotypeR
Commit: 562ab4c84a3687a4f7eb883fd11c8a4fd83e11b6
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-09-13 15:16:43 +0100
Commit message:

  undoing changes to readme.md as this modified via rmd
Package: rhinotypeR
Commit: 91d20661882dfee5163391de3b384d94b59ec288
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-09-13 15:10:33 +0100
Commit message:

 Revert to : undo unwanted commits
 </pre>
    </div>
  
    

      Package: rhinotypeR

      Commit: 4dea2691019c06294f2252212c004601de929b8c

      Author:  Olaitan I. Awe <laitanawe@gmail.com> 

      Date: 2024-11-23 02:21:32 +0100

      Commit message:


	  
		
 how to contribute to rhinotypeR
 

    

  
    

      Package: rhinotypeR

      Commit: f8e640d40a03f11bf155d9ec3fee3ffb59aba9ca

      Author:  Olaitan I. Awe <laitanawe@gmail.com> 

      Date: 2024-11-23 01:53:49 +0100

      Commit message:


	  
		
 how to contribute to rhinotypeR
 

    

  
    

      Package: rhinotypeR

      Commit: 309812f074cb8d9b90c313632abd4e13e756791a

      Author:  Olaitan I. Awe <laitanawe@gmail.com> 

      Date: 2024-11-23 01:53:10 +0100

      Commit message:


	  
		
 how to contribute to rhinotypeR
 

    

  
    

      Package: rhinotypeR

      Commit: bacd8c433420d7e80a2a9a6ca759b3817773dbad

      Author:  Olaitan I. Awe <laitanawe@gmail.com> 

      Date: 2024-11-23 01:50:19 +0100

      Commit message:


	  
		
 how to contribute to rhinotypeR
 

    

  
    

      Package: rhinotypeR

      Commit: 38274db37608cc4720b1dacd6a8fcb18e08c5143

      Author:  marthaluka <mawia.martha@gmail.com> 

      Date: 2024-10-03 17:10:11 +0100

      Commit message:


	  
		
 Merge branch 'main' of https://github.com/omicscodeathon/rhinotypeR
 

    

  
    

      Package: rhinotypeR

      Commit: 5a6bf06537bae9e12ebb42518ada49eacf29c569

      Author:  Martha Luka <39192976+marthaluka@users.noreply.github.com> 

      Date: 2024-09-14 13:40:22 +0100

      Commit message:


	  
		
 Merge pull request #9 from omicscodeathon/devel

Update .gitignore 

    

  
    

      Package: iscream

      Commit: bfe73bbc3086d8d49bd794e4d7f3f95b97d5d790

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-21 11:10:12 -0400

      Commit message:


	  
		
 chore(DESCRIPTION): bump version
 

    

  
    

      Package: iscream

      Commit: e3d33cc30e46432fab36cea2fb7e9f1f5a58296e

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-21 11:16:56 -0400

      Commit message:


	  
		
 test: load required bioc packages to run functions returning them
 

    

  
    

      Package: iscream

      Commit: 6595f1007d77eebc1dbd5e4f4be39449779880ca

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-21 10:44:24 -0400

      Commit message:


	  
		
 !fix(make_mat_gr|tabix_gr): error if the bioc package is not loaded
 

    

  
    

      Package: iscream

      Commit: 38c1ee4b7f199c76207c37012a6c89d5fe027842

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-21 10:43:34 -0400

      Commit message:


	  
		
 fix(make_mat_bsseq): run example iff bsseq is available; namespace the call
 

    

  
    

      Package: iscream

      Commit: 6f10307cdf951995cac2cfa57a8d70b1a1a36570

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-21 10:22:44 -0400

      Commit message:


	  
		
 chore(configure): fix typo in tabix check message
 

    

  
    

      Package: iscream

      Commit: b7822a56cd6ab39f9fa23ca99584b48578a408f2

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-10-21 10:18:49 -0400

      Commit message:


	  
		
 docs(vignettes): add require guards to Suggests
 

    

  
    

      Package: proBatch

      Commit: 2ad0a3808467708f3655e4633a1cf99d887a77f0

      Author:  Yuliya Burankova (Freddsle) <burankova.y@gmail.com> 

      Date: 2025-10-21 17:54:19 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: proBatch

      Commit: 221a2610e018f1f916573bd92d601b3966194999

      Author:  Yuliya Burankova (Freddsle) <burankova.y@gmail.com> 

      Date: 2025-10-21 17:49:04 +0200

      Commit message:


	  
		
 refactor pca plots examples
 

    

  
    

      Package: proBatch

      Commit: b7e535402152c7538e81c5753f55fe6f9eaa1a6c

      Author:  Yuliya Burankova (Freddsle) <burankova.y@gmail.com> 

      Date: 2025-10-21 17:35:18 +0200

      Commit message:


	  
		
 Refactor examples to use subsets of data for faster checks
 

    

  
    

      Package: proBatch

      Commit: 6674936ec70f3f6a410cd7c694ed36d85ac1b926

      Author:  Yuliya Burankova (Freddsle) <burankova.y@gmail.com> 

      Date: 2025-10-21 16:12:29 +0200

      Commit message:


	  
		
 Update vignettes
 

    

  
    

      Package: transmogR

      Commit: 3b27ef9ba4331c1482fdfb182ad8ce4210a3e283

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-10-22 01:35:30 +1030

      Commit message:


	  
		
 Version bump after tweak
 

    

  
    

      Package: transmogR

      Commit: 045877d7a88b1dfbc5015940c5eb3126a27960ef

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-10-22 01:30:54 +1030

      Commit message:


	  
		
 Made overdispFromBoots a public function
 

    

  
    

      Package: transmogR

      Commit: 8b1207fa949f5458e8fd1cc2ad2bf609694115bd

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-10-22 00:45:08 +1030

      Commit message:


	  
		
 Handled missing .ids
 

    

  
    

      Package: pRoloc

      Commit: 2f6ab451c54a39a38d14aac25823b2efbce98006

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-10-21 16:19:03 +0100

      Commit message:


	  
		
 Merge pull request #160 from lgatto/tagm-mcmc-v2

new optimised version of tagm mcmc 

    

  
    

      Package: pRoloc

      Commit: e15a5ccc7ac9f3e7398cd4d772e50a1d480c97d0

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-10-21 16:00:37 +0100

      Commit message:


	  
		
 fix conflicts
 

    

  
    

      Package: pRoloc

      Commit: 3f197d4f106c097f9a0463b693aeaacd825b2e76

      Author:  Oliver M. Crook <ococrook@gmail.com> 

      Date: 2025-10-06 15:15:46 +0100

      Commit message:


	  
		
 update docs
 

    

  
    

      Package: pRoloc

      Commit: 913a4f6bad9ba492e5a7af724865884223650ceb

      Author:  Oliver M. Crook <ococrook@gmail.com> 

      Date: 2025-10-06 15:13:25 +0100

      Commit message:


	  
		
 switch default to new version
 

    

  
    

      Package: pRoloc

      Commit: 3521f8b2b3e1576b29a873e9ff89f78257be917d

      Author:  Oliver M. Crook <ococrook@gmail.com> 

      Date: 2025-09-24 13:44:28 +0100

      Commit message:


	  
		
 clearn RcppExports
 

    

  
    

      Package: pRoloc

      Commit: 3b89c006714b2ae1b04865e1f3452780c2e64790

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-09-24 13:07:55 +0100

      Commit message:


	  
		
 remove pRoloc.so in src
 

    

  
    

      Package: pRoloc

      Commit: dc5f49dc2483da88f155fd4b6fcef6e1ae1eed3f

      Author:  Lisa Breckels <lms79@cam.ac.uk> 

      Date: 2025-09-24 13:07:10 +0100

      Commit message:


	  
		
 remove .o files from src
 

    

  
    

      Package: pRoloc

      Commit: 980963cc480d08b98e0e1daec5d24de7369e3b81

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2025-09-23 19:47:17 +0200

      Commit message:


	  
		
 Merge branch 'devel' into tagm-mcmc-v2 

    

  
    

      Package: pRoloc

      Commit: b344b17bdd53456c2eaec31a44e107fd066a7cfc

      Author:  Oliver M. Crook <ococrook@gmail.com> 

      Date: 2025-09-17 15:08:13 +0100

      Commit message:


	  
		
 new optimised version of tagm mcmc

- reimplemented tagm mcmc to be more memory efficient and speed increases.
 

    

  
    

      Package: smoppix

      Commit: db5e143ba7523d82e7987107c7f8e8aa752ebdaf

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 17:23:35 +0200

      Commit message:


	  
		
 Scale bar adding works
 

    

  
    

      Package: smoppix

      Commit: fda6006f0996fdbb792dfcdbd37b8476d260e564

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 15:57:29 +0200

      Commit message:


	  
		
 revert bad idea
 

    

  
    

      Package: smoppix

      Commit: f149da9fc1c9b103706d14224f2e87dc4e9e97bf

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 15:57:16 +0200

      Commit message:


	  
		
 bad idea
 

    

  
    

      Package: smoppix

      Commit: ad58a3ab33c3bb136296b81985075e9de55efcee

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 15:31:55 +0200

      Commit message:


	  
		
 With tests
 

    

  
    

      Package: smoppix

      Commit: 10c3310c5e73b2c3c3d791b1ea715603de7ef768

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 15:29:08 +0200

      Commit message:


	  
		
 Finetuning the scale bars
 

    

  
    

      Package: smoppix

      Commit: e651c059be0bd1ee9d3ac1adf2ff0fcab9323846

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 14:23:00 +0200

      Commit message:


	  
		
 plotcellsscalebar can be merged
 

    

  
    

      Package: smoppix

      Commit: 7e39df9547cd79efea4bd084d672e77e647650e6

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-21 13:42:03 +0200

      Commit message:


	  
		
 scale bars appear correctly
 

    

  
    

      Package: MSstatsResponse

      Commit: 8bcca9c525023fffcbae7ddb1dccc9674afb55bd

      Author:  Sarah Szvetecz <szvetesa@gmail.com> 

      Date: 2025-10-21 10:14:15 -0400

      Commit message:


	  
		
 fixed bpparam() usage
 

    

  
    

      Package: biomaRt

      Commit: 1fcf101187eb7cccbb34795037934a933ec962e5

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

      Date: 2025-10-21 15:32:03 +0200

      Commit message:


	  
		
 Fix if_not_else lints
 

    

  
    

      Package: EWCE

      Commit: 0de5a8e9ba506c440660a235ab4023788d39fc85

      Author:  Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-10-21 13:48:05 +0100

      Commit message:


	  
		
 Merge pull request #103 from NathanSkene/dep-fixes

Fix ggplot v4 related issues 

    

  
    

      Package: EWCE

      Commit: 920379ddb7cacbe710a6c1f14a84b75dc84c25c2

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-10-21 13:17:54 +0100

      Commit message:


	  
		
 Fix `ggplot v4` breaking changes
 

    

  
    

      Package: EWCE

      Commit: 678ef22518d632bd96cd112112992ad45a02a946

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-10-21 11:32:20 +0100

      Commit message:


	  
		
 Fix test for ggplot output
 

    

  
    

      Package: EWCE

      Commit: 083af093e8f1ff681702a58e3c4e83963feef2bd

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-10-21 10:54:22 +0100

      Commit message:


	  
		
 Update maintainer and documentation
 

    

  
    

      Package: QFeatures

      Commit: 205ad412cc8667a3ce754b25b074f4a24d5882ee

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2025-10-21 12:23:33 +0200

      Commit message:


	  
		
 udate news
 

    

  
    

      Package: QFeatures

      Commit: 6fe240b55cf65b7ad221bd6c3d4052e132077b34

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2025-05-26 18:57:44 +0200

      Commit message:


	  
		
 new devel version
 

    

  
    

      Package: UMI4Cats

      Commit: 2dfa73c06e8b262d3971e694f90f4aaf2d4fe197

      Author:  mireia-bioinfo <mireiarr9@gmail.com> 

      Date: 2025-10-21 12:59:01 +0200

      Commit message:


	  
		
 Add session info
 

    

  
    

      Package: proBatch

      Commit: 05ba72ac3f68004970e0371f8f56f4322114a222

      Author:  Yuliya Burankova (Freddsle) <burankova.y@gmail.com> 

      Date: 2025-10-21 12:57:18 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: UMI4Cats

      Commit: bdc9420a52d3df5b8eebc0188375459c9566c1a0

      Author:  mireia-bioinfo <mireiarr9@gmail.com> 

      Date: 2025-10-21 12:48:56 +0200

      Commit message:


	  
		
 Add OrgDb argument for creating gene annotation (#19)
 

    

  
    

      Package: consICA

      Commit: 3739f03b217c4ef144d37a37afdff4201558d4e6

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2025-10-21 10:56:54 +0200

      Commit message:


	  
		
 [fix][man]getGO(): Example running time on nebbiolo2 + bump version 2.7.3
 

    

  
    

      Package: SpaceTrooper

      Commit: 5c86b34dc2ac512315e8a9da84c0442b804c0bb0

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-21 09:43:10 +0100

      Commit message:


	  
		
 bump version to 99.46
 

    

  
    

      Package: SpaceTrooper

      Commit: 7c7258ca352f406dfe835b08bbf74083aafe4a13

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-21 09:41:41 +0100

      Commit message:


	  
		
 fixing major documentation problems
 

    

  
    

      Package: SpaceTrooper

      Commit: fabb9418b031899ab904d71811c9a6ff55fb7d74

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-21 09:29:09 +0100

      Commit message:


	  
		
 fixing problematic documentation
 

    

  
    

      Package: SpaceTrooper

      Commit: 0f2bf098725a3517941056c86f35efd001c40513

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-20 10:57:13 +0100

      Commit message:


	  
		
 adding more informative error in computeQCScore
 

    

  
    

      Package: SpaceTrooper

      Commit: ecb83432f8972a80eeb39c47e2d770c4102204dc

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-20 10:16:10 +0100

      Commit message:


	  
		
 updating readme
 

    

  
    

      Package: SpaceTrooper

      Commit: 662b7b6b3933d7215ff1ca09c0d368346960c266

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-19 20:23:13 +0100

      Commit message:


	  
		
 fixing cache problems with GHA
 

    

  
    

      Package: SpaceTrooper

      Commit: 7935ccfcd5ae9a0cc69ec0c6051df2026360ac6f

      Author:  Dario <dario.righelli@gmail.com> 

      Date: 2025-10-19 19:19:12 +0100

      Commit message:


	  
		
 fixing spaces in description
 

    

  
    

      Package: notameStats

      Commit: 8a99705e8e6e2bf24feed1fa9ae8b94c4687b66b

      Author:  Atte Lihtamo <98050742+attlih@users.noreply.github.com> 

      Date: 2025-10-21 10:19:29 +0300

      Commit message:


	  
		
 Refactor parallel processing handling in univariate statistics (#1)

Only internal changes to speed up parallel processing, which was painfully slow on Windows machines.

* Refactor parallel processing handling in univariate statistics

* Fix auc computation

* Version bump 

    

  
    

      Package: limma

      Commit: 65741f777afec629be52265ed1aad5a8352436f7

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-10-21 18:24:15 +1100

      Commit message:


	  
		
 limma 3.65.7
- Add `upshot` option for treat()
 

    

  
    

      Package: VariantFiltering

      Commit: cafa29d5ab2fd090e8ce8b349b280316e40bd098

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

      Date: 2025-10-20 22:31:25 -0700

      Commit message:


	  
		
 Fixed unit test for filtering variants by location
 

    

  
    

      Package: plyxp

      Commit: abc76c81f4f6956b60a3cc2a31d931d658f0457d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-10-20 20:24:37 -0700

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: plyxp

      Commit: b79c2fe0a02afeb319f328a915b2734ef4bea4f0

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-10-20 20:23:58 -0700

      Commit message:


	  
		
 update summarize behavior

* `summarize.PlySummarizedExperiment` now allows no assay context
arguments * Improve error handling in across() for `.fns` argument *
Remove requirement for assay context in summarize_se_impl
 

    

  
    

      Package: enrichplot

      Commit: a772cb08a0456a888076308a6e268d8c8e5a0bbd

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-21 09:28:56 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: enrichplot

      Commit: b178c139d2e2444d5d8611da54f8889a2f4f23de

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-09-15 09:54:14 +0800

      Commit message:


	  
		
 fixed for #329
 

    

  
    

      Package: enrichplot

      Commit: f401fa54a4f61753242c75f851182d961fcfe24f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-09-13 18:00:55 +0800

      Commit message:


	  
		
 bug fixed, #329
 

    

  
    

      Package: enrichplot

      Commit: bf86dcdc74316c7ee8d9e7f5fcac7e88392204e6

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-07-16 14:39:42 +0800

      Commit message:


	  
		
 test
 

    

  
    

      Package: enrichplot

      Commit: 945f86af9c25e6abdf85e9a0bfe6a96f62f749ed

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-07-14 14:04:49 +0800

      Commit message:


	  
		
 bug fixed, #328
 

    

  
    

      Package: geomeTriD

      Commit: 35117310c2a6b5e8cc27ed83d06883c3a1131f35

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

      Date: 2025-10-20 20:49:24 -0400

      Commit message:


	  
		
 update readme.
 

    

  
    

      Package: scrapper

      Commit: 39ebc39e8bd488ba48b4358037ba7cffb72d62c8

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

      Date: 2025-10-20 15:36:57 -0700

      Commit message:


	  
		
 Support character and logical vectors in sets= for aggregateAcrossGenes.
 

    

  
    

      Package: scrapper

      Commit: 381e727ef8e42a0807205c7116ed74b7238aa637

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

      Date: 2025-10-20 14:22:34 -0700

      Commit message:


	  
		
 More informative names and error messages for internal utilities.
 

    

  
    

      Package: scrapper

      Commit: 2912b8da91216e5c5e8f5eb420d1001abd355a1c

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

      Date: 2025-10-20 14:10:39 -0700

      Commit message:


	  
		
 Obtain sorted and unique gene set indices for scoreGeneSet.

This is a bit more explicit than coercing everything to a logical vector.
 

    

  
    

      Package: BioCor

      Commit: ea914ce797bb19e8bffc8aa3ba7f3fab326df44f

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-10-21 00:08:50 +0200

      Commit message:


	  
		
 Update example
 

    

  
    

      Package: BioCor

      Commit: 34699c438ce321f6cb538835b537da6854aa50fa

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-10-21 00:08:41 +0200

      Commit message:


	  
		
 Fix url
 

    

  
    

      Package: BioCor

      Commit: a99b8f9305034717fd8484912a1826ccbb2ed4b0

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-10-21 00:08:20 +0200

      Commit message:


	  
		
 Update Roxygen2 version
 

    

  
    

      Package: BioCor

      Commit: 0ee6dcfb92b65bd94eb196119a4e0a39a0731826

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-10-15 20:49:05 +0200

      Commit message:


	  
		
 Warn if NAs are detected: could trigger Bioconductor
 

    

  
    

      Package: BioCor

      Commit: 82d86da311a0cf1483c2885ea18690e0d53df34b

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-10-15 20:48:42 +0200

      Commit message:


	  
		
 Fix CRAN detected issues
 

    

  
    

      Package: BioCor

      Commit: a86f532d32ab121298153c7238a9aaa717a09eaa

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-09-23 23:45:13 +0200

      Commit message:


	  
		
 Increase version number
 

    

  
    

      Package: BioCor

      Commit: 5fdb48dc002a53523ca03a2bd9187b64430e70fc

      Author:  Lluís <lluis.revilla@gmail.com> 

      Date: 2025-09-23 23:44:51 +0200

      Commit message:


	  
		
 Update minimum version requirements
 

    

  
    

      Package: MultiRNAflow

      Commit: abe36dd12ccc1a8b09c0a9adf775a3264084ef50

      Author:  Rodolphe Loubaton <loubaton.rodolphe@gmail.com> 

      Date: 2025-10-20 23:54:39 +0200

      Commit message:


	  
		
 New version: 20251020
 

    

  
  


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