Package: genomation
Type: Package
Title: Summary, annotation and visualization of genomic data
Version: 1.44.0
Author: Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna
        Wreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons
        [ctb], Bozena Mika-Gospodorz [ctb]
Maintainer: Altuna Akalin <aakalin@gmail.com>, Vedran Franke
 <vedran.franke@gmail.com>, Katarzyna Wreczycka
 <katwre@gmail.com>
Description: A package for summary and annotation of genomic intervals.
        Users can visualize and quantify genomic intervals over
        pre-defined functional regions, such as promoters, exons,
        introns, etc. The genomic intervals represent regions with a
        defined chromosome position, which may be associated with a
        score, such as aligned reads from HT-seq experiments, TF
        binding sites, methylation scores, etc. The package can use any
        tabular genomic feature data as long as it has minimal
        information on the locations of genomic intervals. In addition,
        It can use BAM or BigWig files as input.
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
biocViews: Annotation, Sequencing, Visualization, CpGIsland
Encoding: latin1
URL: http://bioinformatics.mdc-berlin.de/genomation/
BugReports: https://github.com/BIMSBbioinfo/genomation/issues
Depends: R (>= 3.5.0), grid
Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table,
        Seqinfo, GenomicRanges (>= 1.31.8), GenomicAlignments (>=
        1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute,
        IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix,
        plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern,
        rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14)
Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown,
        RUnit
Collate: 'combineScoreMatrixList.R' 'documentData.R'
        'genomation-classes.R' 'getRandomEnrichment.R'
        'findFeatureComb.R' 'patternMatrix.R' 'plotMatrix.R'
        'randomizeFeature.R' 'readAnnotate.R' 'readData.R'
        'scoreMatrix.R' 'scoreMatrixBin.R' 'scoreMatrixList.R' 'Ops.R'
        'test_genomation_package.R' 'deprecated_defunct.R'
        'enrichmentMatrix.R' 'RcppExports.R'
LinkingTo: Rcpp
RoxygenNote: 6.0.1.9000
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:40:16 UTC
RemoteUrl: https://github.com/bioc/genomation
RemoteRef: RELEASE_3_23
RemoteSha: fd872d6bd8af82ff7c73afb829089ef432ef6582
NeedsCompilation: yes
Packaged: 2026-04-29 13:49:35 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2026-04-29 13:52:07 UTC; windows
Archs: x64
