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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/crupR/ |
| Package Short Url | https://bioconductor.org/packages/crupR/ |
| Package Downloads Report | Download Stats |