CRAN/E | cinaR

cinaR

A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

Installation

About

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.

github.com/eonurk/cinaR/
Bug report File report

Key Metrics

Version 0.2.3
R ≥ 4.0.0
Published 2022-05-18 712 days ago
Needs compilation? no
License GPL-3
CRAN checks cinaR results

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Maintainer

Maintainer

Onur Karakaslar

eonurkara@gmail.com

Authors

Onur Karakaslar

aut / cre

Duygu Ucar

aut

Material

README
NEWS
Reference manual
Package source

Vignettes

cinaR

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

cinaR archive

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