crupR
This is the released version of crupR; for the devel version, see crupR.
An R package to predict condition-specific enhancers from ChIP-seq data
Bioconductor version: Release (3.23)
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")):Verena Laupert, Martin Vingron. crupR: An R package to predict condition-specific enhancers from ChIP-seq data. doi:10.18129/B9.bioc.crupR, R package version 1.4.0, https://bioconductor.org/packages/crupR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| crupR Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialPeakCalling, FunctionalPrediction, GeneTarget, HistoneModification, PeakDetection, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | crupR_1.4.0.tar.gz |
| Windows Binary (x86_64) | crupR_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | crupR_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | crupR_1.3.0.tgz |
| 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 |