Package: CAGEr
Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing
        data for precise mapping of transcription start sites and
        promoterome mining
Version: 2.19.0
Date: 2025-10-10
Authors@R: 
  c( person("Vanja",   "Haberle",   email = "vanja.haberle@gmail.com",       role = "aut"),
     person("Charles", "Plessy",    email = "charles.plessy@oist.jp",        role = "cre"),
     person("Damir",   "Baranasic", email = "damir.baranasic@lms.mrc.ac.uk", role = "ctb"),
     person("Katalin", "Ferenc",    email = "k.t.ferenc@ncmbm.uio.no",       role = "ctb"),
     person("Sarvesh", "Nikumbh",   email = "s.nikumbh@lms.mrc.ac.uk",       role = "ctb")
  )
Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR,
        data.table, formula.tools, Seqinfo, GenomicAlignments (>=
        1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>=
        1.61.1), ggplot2 (>= 4.0.0), gtools, IRanges (>= 2.18.0),
        KernSmooth, Matrix, memoise, plyr, rlang, Rsamtools (>=
        2.25.1), reshape2, rtracklayer (>= 1.69.1), S4Vectors (>=
        0.27.5), scales, som, stringdist, stringi, SummarizedExperiment
        (>= 1.39.1), utils, vegan, VGAM
Depends: methods, MultiAssayExperiment, R (>= 4.1.0)
Suggests: BSgenome.Dmelanogaster.UCSC.dm3,
        BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18,
        BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,
        DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown
Description: The _CAGEr_ package identifies transcription start sites
        (TSS) and their usage frequency from CAGE (Cap Analysis Gene
        Expression) sequencing data. It normalises raw CAGE tag count,
        clusters TSSs into tag clusters (TC) and aggregates them across
        multiple CAGE experiments to construct consensus clusters (CC)
        representing the promoterome.  CAGEr provides functions to
        profile expression levels of these clusters by cumulative
        expression and rarefaction analysis, and outputs the plots in
        ggplot2 format for further facetting and customisation.  After
        clustering, CAGEr performs analyses of promoter width and
        detects differential usage of TSSs (promoter shifting) between
        samples.  CAGEr also exports its data as genome browser tracks,
        and as R objects for downsteam expression analysis by other
        Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
License: GPL-3
biocViews: Preprocessing, Sequencing, Normalization,
        FunctionalGenomics, Transcription, GeneExpression, Clustering,
        Visualization
Collate: 'Multicore.R' 'CTSS.R' 'CAGEexp.R' 'ClusteringFunctions.R'
        'ClusteringMethods.R' 'CAGEr.R' 'Annotations.R'
        'AggregationMethods.R' 'CAGEfightR.R' 'CAGEr-package.R'
        'Paraclu.R' 'CorrelationMethods.R' 'GetMethods.R'
        'CumulativeDistributionMethods.R' 'Distclu.R' 'ExportMethods.R'
        'ExpressionProfilingMethods.R' 'ImportFunctions.R'
        'SetMethods.R' 'ImportMethods.R' 'MergingMethods.R'
        'NormalizationFunctions.R' 'NormalizationMethods.R'
        'QCmethods.R' 'QuantileWidthMethods.R' 'ResetMethods.R'
        'Richness.R' 'RleDataFrame.R' 'ShiftingFunctions.R'
        'ShiftingMethods.R' 'StrandInvaders.R' 'TSSlogo.R'
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:37:21 UTC
RemoteUrl: https://github.com/bioc/CAGEr
RemoteRef: HEAD
RemoteSha: c01d4229e1b606c88380047db2df194347e2ab3d
NeedsCompilation: no
Packaged: 2026-07-05 00:02:06 UTC; root
Author: Vanja Haberle [aut],
  Charles Plessy [cre],
  Damir Baranasic [ctb],
  Katalin Ferenc [ctb],
  Sarvesh Nikumbh [ctb]
Maintainer: Charles Plessy <charles.plessy@oist.jp>