Package: CAGEfightR
Type: Package
Title: Analysis of Cap Analysis of Gene Expression (CAGE) data using
        Bioconductor
Version: 1.30.0
Author: Malte Thodberg
Maintainer: Malte Thodberg <maltethodberg@gmail.com>
Description: CAGE is a widely used high throughput assay for measuring
        transcription start site (TSS) activity. CAGEfightR is an
        R/Bioconductor package for performing a wide range of common
        data analysis tasks for CAGE and 5'-end data in general. Core
        functionality includes: import of CAGE TSSs (CTSSs), tag (or
        unidirectional) clustering for TSS identification,
        bidirectional clustering for enhancer identification,
        annotation with transcript and gene models, correlation of TSS
        and enhancer expression, calculation of TSS shapes,
        quantification of CAGE expression as expression matrices and
        genome brower visualization.
URL: https://github.com/MalteThodberg/CAGEfightR
BugReports: https://github.com/MalteThodberg/CAGEfightR/issues
Depends: R (>= 3.5), GenomicRanges (>= 1.61.1), rtracklayer (>=
        1.69.1), SummarizedExperiment (>= 1.39.1)
Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3),
        Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>=
        0.16.0), IRanges(>= 2.12.0), Seqinfo, GenomicFeatures(>=
        1.61.4), GenomicAlignments(>= 1.45.1), BiocParallel(>= 1.12.0),
        GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>=
        1.9.4), GenomicInteractions(>= 1.15.1)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db,
        TxDb.Mmusculus.UCSC.mm9.knownGene
VignetteBuilder: knitr
biocViews: Software, Transcription, Coverage, GeneExpression,
        GeneRegulation, PeakDetection, DataImport, DataRepresentation,
        Transcriptomics, Sequencing, Annotation, GenomeBrowsers,
        Normalization, Preprocessing, Visualization
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev libjpeg-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 14:45:17 UTC
RemoteUrl: https://github.com/bioc/CAGEfightR
RemoteRef: RELEASE_3_22
RemoteSha: eda75c39e6a04b9c24c3f633546c9ad94f5d40e6
NeedsCompilation: no
Packaged: 2025-11-11 14:28:42 UTC; root
Built: R 4.5.2; ; 2025-11-11 14:38:27 UTC; windows
