Package: crupR
Type: Package
Title: An R package to predict condition-specific enhancers from
        ChIP-seq data
Version: 1.2.0
Authors@R: c(
   person("Persia", "Akbari Omgba", email = "omgba@molgen.mpg.de", role = c("cre")),
   person("Verena", "Laupert", role = c("aut")),
   person("Martin", "Vingron", email = "vingron@molgen.ppg.com", role = c("aut")))
Description: 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.
License: GPL-3
Encoding: UTF-8
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
Depends: R (>= 4.4.0)
Suggests: GenomeInfoDb, testthat, BiocStyle, knitr, rmarkdown
biocViews: DifferentialPeakCalling, GeneTarget, FunctionalPrediction,
        HistoneModification, PeakDetection
BiocType: Software
URL: https://github.com/akbariomgba/crupR
BugReports: https://github.com/akbariomgba/crupR/issues
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:36:29 UTC
RemoteUrl: https://github.com/bioc/crupR
RemoteRef: RELEASE_3_22
RemoteSha: 01667b76a576de2d1952e4af5dbc843039612889
NeedsCompilation: no
Packaged: 2026-01-24 20:44:05 UTC; root
Author: Persia Akbari Omgba [cre],
  Verena Laupert [aut],
  Martin Vingron [aut]
Maintainer: Persia Akbari Omgba <omgba@molgen.mpg.de>
Built: R 4.5.2; ; 2026-01-24 20:48:02 UTC; windows
