chromVAR
Chromatin Variation Across Regions
Bioconductor version: 3.23 · Package version: 1.34.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chromVAR")Details
| Maintainer | Alicia Schep <aschep@gmail.com> |
| Author | Alicia Schep [aut, cre], Jason Buenrostro [ctb], Caleb Lareau [ctb], William Greenleaf [ths], Stanford University [cph] |
| License | MIT + file LICENSE |
| System Requirements | C++14 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/chromVAR/ |
Citation
From within R, enter citation("chromVAR"):
Alicia Schep. chromVAR: Chromatin Variation Across Regions. doi:10.18129/B9.bioc.chromVAR, R package version 1.34.1, https://bioconductor.org/packages/chromVAR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | chromVAR_1.34.1.tar.gz |
| Windows binary (x86_64) | chromVAR_1.34.1.zip |
| macOS binary (arm64) | chromVAR_1.34.1.tgz |
| macOS binary (x86_64) | chromVAR_1.34.1.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: IRanges, Seqinfo, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, pwalign, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome
LinkingTo: Rcpp, RcppArmadillo
Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr