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  [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-devel (arm64): not available, r-release (arm64): not available, r-oldrel (arm64): cinaR_0.2.3.tgz, r-devel (x86_64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
| Old sources: | cinaR archive |
Linking:
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