DOI: 10.18129/B9.bioc.chromVAR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see chromVAR.

Chromatin Variation Across Regions

Bioconductor version: 3.8

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")):


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biocViews GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software
Version 1.4.1
In Bioconductor since BioC 3.6 (R-3.4) (1.5 years)
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
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