Package: IsoformSwitchAnalyzeR
Type: Package
Title: Identify, Annotate and Visualize Alternative Splicing and
        Isoform Switches with Functional Consequences from both short-
        and long-read RNA-seq data.
Version: 1.16.0
Authors@R: person(given="Kristoffer",family="Vitting-Seerup", role=c("cre","aut"),email="k.vitting.seerup@gmail.com",comment = c(ORCID = "0000-0002-6450-0608"))
Description: Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
URL: http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
BugReports: https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
License: GPL (>= 2)
Depends: R (>= 3.6), limma, DEXSeq, ggplot2
Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>=
        2.50.0), IRanges, GenomicRanges, DRIMSeq, RColorBrewer,
        rtracklayer, VennDiagram, DBI, grDevices, graphics, stats,
        utils, GenomeInfoDb, grid, tximport (>= 1.7.1), tximeta (>=
        1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr,
        tibble, XVector, BiocGenerics, RCurl, Biobase
Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown
VignetteBuilder: knitr
Collate: classes.R methods.R import_data.R test_isoform_switches.R
        analyze_ORF.R analyze_external_sequence_analysis.R
        analyze_switch_consequences.R isoform_plots.R
        plot_all_iso_switch.R high_level_functions.R tools.R
        analyze_alternative_splicing.R
biocViews: GeneExpression, Transcription, AlternativeSplicing,
        DifferentialExpression, DifferentialSplicing, Visualization,
        StatisticalMethod, TranscriptomeVariant, BiomedicalInformatics,
        FunctionalGenomics, SystemsBiology, Transcriptomics, RNASeq,
        Annotation, FunctionalPrediction, GenePrediction, DataImport,
        MultipleComparison, BatchEffect, ImmunoOncology
RoxygenNote: 6.0.1
git_url: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
git_branch: RELEASE_3_14
git_last_commit: 5eb5b2b
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
NeedsCompilation: yes
Packaged: 2021-10-26 21:47:19 UTC; biocbuild
Author: Kristoffer Vitting-Seerup [cre, aut]
    (<https://orcid.org/0000-0002-6450-0608>)
Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Built: R 4.1.1; x86_64-conda-linux-gnu; 2021-11-08 04:42:22 UTC; unix
