Package: IsoformSwitchAnalyzeR
Type: Package
Title: An R package to Identify, Annotate and Visualize Isoform
        Switches with Functional Consequences (from RNA-seq data)
Version: 1.2.0
Author: Kristoffer Vitting-Seerup
Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Description: IsoformSwitchAnalyzeR enables identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.
URL: http://bioconductor.org/packages/IsoformSwitchAnalyzeR/
BugReports: https://github.com/kvittingseerup/IsoformSwitchAnalyzeR/issues
License: GPL (>= 2)
Depends: R (>= 3.4), cummeRbund
Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings,
        IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer,
        ggplot2, VennDiagram, DBI, grDevices, graphics, stats, utils,
        GenomeInfoDb, grid, tximport, edgeR, futile.logger
Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19
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, Sequencing,
        Visualization, StatisticalMethod, TranscriptomeVariant,
        BiomedicalInformatics, FunctionalGenomics, SystemsBiology,
        Transcriptomics, RNASeq, Annotation, FunctionalPrediction,
        GenePrediction, DataImport, MultipleComparison
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2018-05-01 01:30:42 UTC; biocbuild
Built: R 3.4.1; x86_64-apple-darwin14.5.0; 2018-10-21 16:05:34 UTC; unix
