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: 1.8.0
Author: Kristoffer Vitting-Seerup
Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Description: IsoformSwitchAnalyzeR enables identification and 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, Cufflinks/Cuffdiff, RSEM etc.
URL: http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
BugReports: https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
License: GPL (>= 2)
Depends: R (>= 3.5), 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), edgeR,
        futile.logger, stringr, dplyr, magrittr, readr, XVector
Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund
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_10
git_last_commit: 2ad64ab
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: yes
Packaged: 2019-10-30 02:37:08 UTC; biocbuild
Built: R 3.6.1; x86_64-apple-darwin13.4.0; 2019-11-01 15:30:52 UTC; unix
