chromVAR
This is the released version of chromVAR; for the devel version, see chromVAR.
Chromatin Variation Across Regions
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.34.1 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | IRanges, Seqinfo, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, pwalign, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome |
| System Requirements | C++14 |
| 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_1.34.1.tar.gz |
| Windows Binary (x86_64) | chromVAR_1.34.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | chromVAR_1.34.1.tgz |
| macOS Binary (sonoma-arm64) | chromVAR_1.34.1.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 |