crupR (original) (raw)

This is the released version of crupR; for the devel version, seecrupR.

An R package to predict condition-specific enhancers from ChIP-seq data

Bioconductor version: Release (3.21)

An R package that offers a workflow to predict condition-specific enhancers from ChIP-seq data. The prediction of regulatory units is done in four main steps: Step 1 - the normalization of the ChIP-seq counts. Step 2 - the prediction of active enhancers binwise on the whole genome. Step 3 - the condition-specific clustering of the putative active enhancers. Step 4 - the detection of possible target genes of the condition-specific clusters using RNA-seq counts.

Author: Persia Akbari Omgba [cre], Verena Laupert [aut], Martin Vingron [aut]

Maintainer: Persia Akbari Omgba

Citation (from within R, enter citation("crupR")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("crupR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crupR")

Details

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Follow Installation instructions to use this package in your R session.