iscream
This is the development version of iscream; to use it, please install the devel version of Bioconductor.
Make fast and memory efficient BED file queries, summaries and matrices
Bioconductor version: Development (3.22)
BED files store ranged genomic data that can be queried even when the files are compressed. iscream can query data from BED files and return them in muliple formats: parsed records or their summary statistics as data frames or GenomicRanges objects, and matrices as matrix, GenomicRanges, or SummarizedExperiment objects. iscream also provides specialized support for importing methylation data.
Author: James Eapen [aut, cre]
, Jacob Morrison [aut]
, Nathan Spix [ctb], Hui Shen [aut, ths, fnd]
Maintainer: James Eapen <james.eapen at vai.org>
citation("iscream")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("iscream")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DNAMethylation, DataImport, Sequencing, SingleCell, Software |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5) |
| Imports | Rcpp, Matrix, data.table, methods, pbapply, parallelly, stringfish |
| System Requirements | htslib: htslib-devel (rpm) or libhts-dev (deb) & tabix: htslib-tools (rpm) or tabix (deb) & GNU make |
| URL | https://huishenlab.github.io/iscream/ https://github.com/huishenlab/iscream/ |
| Bug Reports | https://github.com/huishenlab/iscream/issues/ |
See More
| Suggests | BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr, microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools, SummarizedExperiment, S4Vectors, testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppArmadillo, RcppProgress, RcppSpdlog, Rhtslib, stringfish |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | iscream_0.99.8.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iscream |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iscream |
| Bioc Package Browser | https://code.bioconductor.org/browse/iscream/ |
| Package Short Url | https://bioconductor.org/packages/iscream/ |
| Package Downloads Report | Download Stats |