DOI: 10.18129/B9.bioc.chromVAR    

This is the development version of chromVAR; for the stable release version, see chromVAR.

Chromatin Variation Across Regions

Bioconductor version: Development (3.7)

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>

Citation (from within R, enter citation("chromVAR")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script Introduction
PDF   Reference Manual
Text   NEWS


biocViews GeneRegulation, Sequencing, SingleCell, Software
Version 1.1.1
License MIT + file LICENSE
Depends R (>= 3.4)
Imports IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, 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
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package chromVAR_1.1.1.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) chromVAR_1.1.1.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: