crupR
This is thereleased version of crupR; for the devel version, seecrupR.
An R package to predict condition-specific enhancers from ChIP-seq data
Bioconductor version: Release (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("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 appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("crupR")| crupR Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialPeakCalling,FunctionalPrediction,GeneTarget,HistoneModification,PeakDetection,Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | bamsignals,Rsamtools,GenomicRanges,preprocessCore,randomForest,rtracklayer,Seqinfo,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 |
See More
| Suggests | GenomeInfoDb,testthat,BiocStyle,knitr,rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | crupR_1.2.0.tar.gz |
| Windows Binary (x86_64) | crupR_1.2.0.zip |
| macOS Binary (x86_64) | crupR_1.2.0.tgz |
| macOS Binary (arm64) | crupR_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crupR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crupR |
| Bioc Package Browser | https://code.bioconductor.org/browse/crupR/ |
| Package Short Url | https://bioconductor.org/packages/crupR/ |
| Package Downloads Report | Download Stats |