Package: cinaR
Type: Package
Title: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Version: 0.2.6
Authors@R: 
    c(person(given = "Onur",
             family = "Karakaslar",
             role = c("aut", "cre"),
             email = "eonurkara@gmail.com",
             comment = c(ORCID = "0000-0002-9182-910X")),
      person(given = "Duygu",
             family = "Ucar",
             role = "aut",
             comment = c(ORCID = "0000-0002-9772-3066"))
      )
Author: Onur Karakaslar [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9182-910X>),
  Duygu Ucar [aut] (ORCID: <https://orcid.org/0000-0002-9772-3066>)
Maintainer: Onur Karakaslar <eonurkara@gmail.com>
Description: 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>.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/eonurk/cinaR/, https://eonurk.github.io/cinaR/
BugReports: https://github.com/eonurk/cinaR/issues/
biocViews:
Depends: R (>= 4.0.0)
Imports: BiocManager, DESeq2, dplyr, edgeR, fgsea, GenomicRanges,
        ggplot2, ggrepel, grDevices, limma, methods, utils, pheatmap,
        preprocessCore, RColorBrewer, sva, writexl
RoxygenNote: 7.2.3
Suggests: ChIPseeker, knitr, Matrix, Seurat, rmarkdown, markdown,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene
VignetteBuilder: knitr, rmarkdown, markdown
NeedsCompilation: no
Packaged: 2026-02-04 14:02:40 UTC; onur-lumc
Repository: CRAN
Date/Publication: 2026-02-04 14:50:02 UTC
Built: R 4.5.3; ; 2026-03-22 04:00:03 UTC; windows
