Package: CAGEr
Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing
        data for precise mapping of transcription start sites and
        promoterome mining
Version: 1.30.3
Date: 2020-07-14
Author: Vanja Haberle <vanja.haberle@gmail.com>
Maintainer: Vanja Haberle <vanja.haberle@gmail.com>, Charles Plessy <charles.plessy@oist.jp>, Damir Baranasic <damir.baranasic@lms.mrc.ac.uk>, Sarvesh Nikumbh <s.nikumbh@lms.mrc.ac.uk>
Imports: beanplot, BiocGenerics, BiocParallel, BSgenome, data.table,
        DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments,
        GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges
        (>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape,
        rtracklayer, S4Vectors, som, stringdist, stringi,
        SummarizedExperiment, utils, vegan, VGAM
Depends: methods, MultiAssayExperiment, R (>= 3.5.0)
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: 'CTSS.R' 'CAGEexp.R' 'AllClasses.R' 'CAGEr.R'
        'AggregationFunctions.R' 'Multicore.R' 'ClusteringFunctions.R'
        'ClusteringMethods.R' 'Annotations.R' 'AggregationMethods.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' 'QuantileWidthFunctions.R'
        'QuantileWidthMethods.R' 'Richness.R' 'ShiftingFunctions.R'
        'ShiftingMethods.R' 'StrandInvaders.R'
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE)
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_11
git_last_commit: 3cc7af7
git_last_commit_date: 2020-07-14
Date/Publication: 2020-07-14
NeedsCompilation: no
Packaged: 2020-07-15 02:04:46 UTC; biocbuild
Built: R 4.0.2; ; 2020-07-15 15:57:40 UTC; windows
