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cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles (original) (raw)

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
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

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