Package: cinaR
Type: Package
Title: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Version: 0.2.3
Authors@R: 
    c(person(given = "Onur",
             family = "Karakaslar",
             role = c("aut", "cre"),
             email = "eonurkara@gmail.com"),
      person(given = "Duygu",
             family = "Ucar",
             role = "aut",
             comment = c(ORCID = "0000-0002-9772-3066"))
      )
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/
BugReports: https://github.com/eonurk/cinaR/issues/
biocViews:
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
RoxygenNote: 7.1.2
Suggests: knitr, rmarkdown, markdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-17 08:45:32 UTC; onur-lumc
Author: Onur Karakaslar [aut, cre],
  Duygu Ucar [aut] (<https://orcid.org/0000-0002-9772-3066>)
Maintainer: Onur Karakaslar <eonurkara@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 14:00:09 UTC
Built: R 4.5.1; ; 2025-10-06 02:50:20 UTC; windows
