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Bioconductor - chromVAR

chromVAR

This is the released version of chromVAR; for the devel version, see chromVAR.

Chromatin Variation Across Regions

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("chromVAR")
Details biocViews GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software Version 1.30.1 In Bioconductor since BioC 3.6 (R-3.4) (7.5 years) License MIT + file LICENSE Depends R (>= 3.5.0) 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 System Requirements C++11 URL See More Package Archives

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

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