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README.md
In cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
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
License
- GNU General Public License v3.0
Try the cinaR package in your browser
Any scripts or data that you put into this service are public.
cinaR documentation built on May 18, 2022, 5:12 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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
License
- GNU General Public License v3.0
Try the cinaR package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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