DESCRIPTION

Package: IsoformSwitchAnalyzeR
Type: Package
Title: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Version: 2.1.4
Authors@R: c(person(given="Kristoffer",family="Vitting-Seerup", role=c("cre","aut"),email="k.vitting.seerup@gmail.com",comment = c(ORCID = "0000-0002-6450-0608")), person(given="Chunxu",family="Han", role="ctb",email="chunxuhan007@gmail.com"), person(given="Jeroen",family="Gilis", role="ctb", email="jeroen.gilis@ugent.be",comment = c(ORCID = "0000-0001-8415-0943")))
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
    RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.
URL: http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
BugReports: https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
License: GPL (>= 2)
Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR
Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges,
    GenomicRanges, 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,
    SummarizedExperiment, tidyr, S4Vectors, BiocParallel
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: 7.2.3