betterChromVAR
Improved ChromVAR (Chromatin Variation Across Regions)
Bioconductor version: 3.24 · Package version: 1.1.10
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
A much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("betterChromVAR")Details
| Maintainer | Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch> |
| Author | Pierre-Luc Germain [aut, cre] (ORCID: <https://orcid.org/0000-0003-3418-4218>) |
| License | GPL (>= 3) |
| URL | https://github.com/plger/betterChromVAR |
| Bug Reports | https://github.com/plger/betterChromVAR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, Epigenetics, Normalization, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/betterChromVAR/ |
Citation
From within R, enter citation("betterChromVAR"):
Pierre-Luc Germain. betterChromVAR: Improved ChromVAR (Chromatin Variation Across Regions). doi:10.18129/B9.bioc.betterChromVAR, R package version 1.1.10, https://bioconductor.org/packages/betterChromVAR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | betterChromVAR_1.1.10.tar.gz |
| Windows binary (x86_64) | betterChromVAR_1.1.10.zip |
| macOS binary (arm64) | betterChromVAR_1.1.10.tgz |
| macOS binary (x86_64) | betterChromVAR_1.1.10.tgz |
Dependencies
Depends: R (>= 4.1.0), SummarizedExperiment
Imports: BiocParallel, BiocNeighbors, Biostrings, DelayedMatrixStats, GenomicRanges, IRanges, Matrix, matrixStats, sparseMatrixStats, MatrixGenerics, methods, S4Vectors, stats
Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat