chromVAR
This is the released version of chromVAR; for the devel version, see chromVAR.
All Bioconductor versions of chromVAR
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
Chromatin Variation Across Regions
Bioconductor version: 3.23 · Package version: 1.34.1
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.
Author: Alicia Schep [aut, cre], Jason Buenrostro [ctb], Caleb Lareau [ctb], William Greenleaf [ths], Stanford University [cph]
Maintainer: Alicia Schep <aschep at gmail.com>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chromVAR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.34.1 |
| License | MIT + file LICENSE |
| System Requirements | C++14 |
| Last updated | 2026-05-08 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 219 of 2,418 |
| 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/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("chromVAR")| chromVAR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| Source Repository | git clone https://git.bioconductor.org/packages/chromVAR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/chromVAR |
| Package Downloads Report | Download Stats |
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