Package: IsoformSwitchAnalyzeR
Type: Package
Title: An R package to Identify, Annoatate and Visialize Isoform
        Switches with Functional Consequences (from RNA-seq data)
Version: 1.0.0
Author: Kristoffer Vitting-Seerup
Maintainer: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Description: IsoformSwitchAnalyzeR enabels 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, spliceR
Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings,
        IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer,
        ggplot2, VennDiagram, DBI, grDevices, graphics, stats, utils,
        GenomeInfoDb, grid, tximport, edgeR
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
        intron_retention.R analyze_switch_consequences.R
        isoform_plots.R plot_all_iso_switch.R high_level_functions.R
        tools.R extractGenomeWideAnalysis.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: no
Packaged: 2017-10-31 01:26:58 UTC; biocbuild
Built: R 3.4.1; ; 2017-12-06 15:11:12 UTC; unix
