chromVAR
Chromatin Variation Across Regions
Bioconductor version: Release (3.19)
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("chromVAR")
):
Installation
To install this package, start R (version "4.4") 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")
Introduction | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | GeneRegulation, ImmunoOncology, Sequencing, SingleCell, Software |
Version | 1.26.0 |
In Bioconductor since | BioC 3.6 (R-3.4) (7 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
Suggests | JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr |
Linking To | Rcpp, RcppArmadillo |
Enhances | |
Depends On Me | |
Imports Me | ATACCoGAPS |
Suggests Me | MOCHA, Signac |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | chromVAR_1.26.0.tar.gz |
Windows Binary | chromVAR_1.26.0.zip |
macOS Binary (x86_64) | chromVAR_1.26.0.tgz |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/chromVAR |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/chromVAR |
Bioc Package Browser | https://code.bioconductor.org/browse/chromVAR/ |
Package Short Url | https://bioconductor.org/packages/chromVAR/ |
Package Downloads Report | Download Stats |