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cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.

Version: 0.2.3
Depends: R (≥ 4.0.0)
Imports: ChIPseeker, DESeq2, dplyr, edgeR, fgsea, GenomicRanges, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, ggplot2, ggrepel, grDevices, limma, utils, pheatmap, preprocessCore, RColorBrewer, sva, writexl
Suggests: knitr, rmarkdown, markdown
Published: 2022-05-18
DOI: 10.32614/CRAN.package.cinaR
Author: Onur Karakaslar [aut, cre], Duygu Ucar ORCID iD [aut]
Maintainer: Onur Karakaslar <eonurkara at gmail.com>
BugReports: https://github.com/eonurk/cinaR/issues/
License: GPL-3
URL: https://github.com/eonurk/cinaR/
NeedsCompilation: no
Materials: README NEWS
CRAN checks: cinaR results

Documentation:

Reference manual: cinaR.pdf
Vignettes: cinaR

Downloads:

Package source: cinaR_0.2.3.tar.gz
Windows binaries: r-devel: cinaR_0.2.3.zip, r-release: cinaR_0.2.3.zip, r-oldrel: cinaR_0.2.3.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): cinaR_0.2.3.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available
Old sources: cinaR archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=cinaR to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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