In eonurk/cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/",
  out.width = "100%",
  fig.dpi = 96
)

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")

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"))

Usage

knitr::opts_chunk$set(dpi=300,fig.width=6)

library(cinaR)

# create contrast vector which will be compared.
contrasts<- c("B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO", 
              "B6", "B6", "B6", "B6", "B6", "NZO", "NZO", "NZO", "NZO", "NZO", "NZO")

# If reference genome is not set hg38 will be used!
results <- cinaR(bed, contrasts, reference.genome = "mm10")

pca_plot(results, contrasts, show.names = F)

For more details please go to our site from here!

Citation

@article {Karakaslar2021.03.05.434143,
    author = {Karakaslar, E Onur and Ucar, Duygu},
    title = {cinaR: A comprehensive R package for the differential analyses and 
    functional interpretation of ATAC-seq data},
    year = {2021},
    doi = {10.1101/2021.03.05.434143},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2021/03/08/2021.03.05.434143.1},
    journal = {bioRxiv}
}