chromVAR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see chromVAR.
Chromatin Variation Across Regions
Bioconductor version: 3.9
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 "3.6") 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.
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 | 1.6.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | chromVAR_1.6.0.tar.gz |
| Windows Binary | chromVAR_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | chromVAR_1.6.0.tgz |
| 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 |
| Old Source Packages for BioC 3.9 | Source Archive |