crupR
This is the development version of crupR; to use it, please install the devel version of Bioconductor.
An R package to predict condition-specific enhancers from ChIP-seq data
Bioconductor version: Development (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 <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")
# 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
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 | 0.99.4 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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 |
See More
| 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 | crupR_0.99.4.tar.gz |
| Windows Binary (x86_64) | crupR_0.99.4.zip (64-bit only) |
| macOS Binary (x86_64) | crupR_0.99.4.tgz |
| macOS Binary (arm64) | crupR_0.99.4.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 |