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: | 0.2.6 |
| Depends: | R (≥ 4.0.0) |
| Imports: | BiocManager, DESeq2, dplyr, edgeR, fgsea, GenomicRanges, ggplot2, ggrepel, grDevices, limma, methods, utils, pheatmap, preprocessCore, RColorBrewer, sva, writexl |
| Suggests: | ChIPseeker, knitr, Matrix, Seurat, rmarkdown, markdown, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene |
| Published: | 2026-02-04 |
| DOI: | 10.32614/CRAN.package.cinaR |
| Author: | Onur Karakaslar 
[aut, cre],
Duygu Ucar [aut] |
| Maintainer: | Onur Karakaslar <eonurkara at gmail.com> |
| BugReports: | https://github.com/eonurk/cinaR/issues/ |
| License: | GPL-3 |
| URL: | https://github.com/eonurk/cinaR/, https://eonurk.github.io/cinaR/ |
| NeedsCompilation: | no |
| Citation: | cinaR citation info |
| Materials: | README, NEWS |
| CRAN checks: | cinaR results |
Documentation:
| Reference manual: | cinaR.html , cinaR.pdf |
| Vignettes: |
cinaR (source, R code) |
Downloads:
| Package source: | cinaR_0.2.6.tar.gz |
| Windows binaries: | r-devel: cinaR_0.2.6.zip, r-release: cinaR_0.2.6.zip, r-oldrel: cinaR_0.2.6.zip |
| macOS binaries: | r-release (arm64): cinaR_0.2.6.tgz, r-oldrel (arm64): cinaR_0.2.6.tgz, r-release (x86_64): cinaR_0.2.6.tgz, r-oldrel (x86_64): cinaR_0.2.6.tgz |
| Old sources: | cinaR archive |
Linking:
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