cmf1997 / cinar-cmf

A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)

cinaR

Overview

cinaR is a single wrapper function for end-to-end computational analyses of bulk ATAC-seq (or RNA-seq) profiles. Starting from a consensus peak file, it outputs differentially accessible peaks, enrichment results, and provides users with various configurable visualization options. For more details, please see the preprint.

Installation

# CRAN mirror
install.packages("cinaR")

Development version

To get bug fix and use a feature from the development version:

# install.packages("devtools")
devtools::install_github("eonurk/cinaR")

Usage

For more details please go to our site from here!

Known Installation Issues

Sometimes bioconductor related packages may not be installed automatically.
Therefore, you may need to install them manually:

BiocManager::install(c("ChIPseeker", "DESeq2", "edgeR", "fgsea","GenomicRanges", "limma", "preprocessCore", "sva", "TxDb.Hsapiens.UCSC.hg38.knownGene", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Mmusculus.UCSC.mm10.knownGene"))

Contribution

You can send pull requests to make your contributions.

Author

• E Onur Karakaslar

License

• GNU General Public License v3.0