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: 0.2.1
Depends: R (≥ 3.5.0)
Imports: ChIPseeker, DESeq2, dplyr, edgeR, fgsea, GenomicRanges, ggplot2, ggrepel, grDevices, limma, utils, pheatmap, preprocessCore, RColorBrewer, sva, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, writexl
Suggests: biomaRt, knitr, rmarkdown
Published: 2021-04-02
Author: Onur Karakaslar [aut, cre], Duygu Ucar ORCID iD [aut]
Maintainer: Onur Karakaslar <eonurkara at>
License: GPL-3
NeedsCompilation: no
Materials: README NEWS
CRAN checks: cinaR results


Reference manual: cinaR.pdf
Vignettes: cinaR


Package source: cinaR_0.2.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): not available, r-release (x86_64): not available, r-oldrel: not available
Old sources: cinaR archive


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