Package: FRASER
Type: Package
Title: Find RAre Splicing Events in RNA-Seq Data
Version: 1.4.0
Date: 2021-01-27
Authors@R: c(
    person("Christian", "Mertes", role=c("aut", "cre"), 
            email="mertes@in.tum.de"),
    person("Ines", "Scheller",  role=c("aut"), email="scheller@in.tum.de"),
    person("Vicente", "Yepez", role=c("ctb"), email="yepez@in.tum.de"),
    person("Julien", "Gagneur", role=c("aut"), email="gagneur@in.tum.de"))
Description: Detection of rare aberrant splicing events in transcriptome 
    profiles. The workflow aims to assist the diagnostics in the field of 
    rare diseases where RNA-seq is performed to identify aberrant 
    splicing defects.
biocViews: RNASeq, AlternativeSplicing, Sequencing, Software, Genetics,
        Coverage
License: MIT + file LICENSE
URL: https://github.com/gagneurlab/FRASER
BugRepots: https://github.com/gagneurlab/FRASER/issues
RoxygenNote: 7.1.1
Encoding: UTF-8
VignetteBuilder: knitr
Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment
Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt,
        BSgenome, cowplot, DelayedArray (>= 0.5.11),
        DelayedMatrixStats, extraDistr, generics, GenomeInfoDb,
        GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges,
        grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods,
        OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer,
        rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools,
        utils, VGAM
Suggests: BiocStyle, knitr, rmarkdown, testthat, covr,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
LinkingTo: Rcpp, RcppArmadillo
Collate: variables.R getNSetterFuns.R FRASER-package.R
        FraserDataSet-class.R AllGenerics-definitions.R AllGenerics.R
        Fraser-pipeline.R annotationOfRanges.R beta-binomial-testing.R
        calculatePSIValue.R countRNAseqData.R example_functions.R
        filterExpression.R find_encoding_dimensions.R getURLs.R
        helper-functions.R mergeExternalData.R saveHDF5Objects.R
        RcppExports.R autoencoder.R updateD.R updateE.R updateRho.R
        pvalsNzscore.R makeSimulatedDataset.R fitCorrectionMethods.R
        plotMethods.R zzz.R
git_url: https://git.bioconductor.org/packages/FRASER
git_branch: RELEASE_3_13
git_last_commit: 926f313
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: yes
Packaged: 2021-05-20 00:13:09 UTC; biocbuild
Author: Christian Mertes [aut, cre],
  Ines Scheller [aut],
  Vicente Yepez [ctb],
  Julien Gagneur [aut]
Maintainer: Christian Mertes <mertes@in.tum.de>
Built: R 4.1.0; i386-w64-mingw32; 2021-05-20 08:10:24 UTC; windows
Archs: i386, x64
