crupR

This is the development version of crupR; for the stable release version, see crupR.

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

Bioconductor version: Development (3.22)

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 <omgba at molgen.mpg.de>

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("crupR")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialPeakCalling, FunctionalPrediction, GeneTarget, HistoneModification, PeakDetection, Software
Version	1.1.0
In Bioconductor since	BioC 3.21 (R-4.5) (< 6 months)
License	GPL-3
Depends	R (>= 4.4.0)
Imports	bamsignals, Rsamtools, GenomicRanges, preprocessCore, randomForest, rtracklayer, GenomeInfoDb, S4Vectors, ggplot2, matrixStats, dplyr, IRanges, GenomicAlignments, GenomicFeatures, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, reshape2, magrittr, stats, utils, grDevices, SummarizedExperiment, BiocParallel, fs, methods
System Requirements
URL	https://github.com/akbariomgba/crupR
Bug Reports	https://github.com/akbariomgba/crupR/issues

Suggests	testthat, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/crupR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/crupR
Package Short Url	https://bioconductor.org/packages/crupR/
Package Downloads Report	Download Stats