Package: CAGEr
Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing
        data for precise mapping of transcription start sites and
        promoterome mining
Version: 2.10.0
Date: 2023-10-07
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("Sarvesh", "Nikumbh",   email = "s.nikumbh@lms.mrc.ac.uk",       role = "ctb")
  )
Imports: BiocGenerics, BiocParallel, BSgenome, CAGEfightR, data.table,
        DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb,
        GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>=
        2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr,
        Rsamtools, reshape2, rtracklayer, S4Vectors (>= 0.27.5), som,
        stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM
Depends: methods, MultiAssayExperiment, R (>= 4.1.0)
Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE,
        BiocStyle, knitr, rmarkdown
Description: Preprocessing of CAGE sequencing data, identification and
 normalization of transcription start sites and downstream analysis of
 transcription start sites clusters (promoters).
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' 'CorrelationMethods.R'
        'CumulativeDistributionFunctions.R' 'GetMethods.R'
        'CumulativeDistributionMethods.R' 'ExportFunctions.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'
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.2.1
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_19
git_last_commit: 6c8b145
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 21:38:44 UTC; biocbuild
Author: Vanja Haberle [aut],
  Charles Plessy [cre],
  Damir Baranasic [ctb],
  Sarvesh Nikumbh [ctb]
Maintainer: Charles Plessy <charles.plessy@oist.jp>
Built: R 4.4.0; ; 2024-05-02 12:32:24 UTC; windows
