Package: FRASER
Type: Package
Title: Find RAre Splicing Events in RNA-Seq Data
Version: 1.0.1
Date: 2020-06-08
Author: Christian Mertes <mertes@in.tum.de>, Ines Scheller <scheller@in.tum.de>,
    Prof. Julien Gagneur <gagneur@in.tum.de>
Maintainer: Christian Mertes <mertes@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.
License: MIT + file LICENSE
Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment
Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt,
        BSgenome, cowplot, DelayedArray (>= 0.5.11),
        DelayedMatrixStats, extraDistr, GenomeInfoDb,
        GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges,
        grDevices, ggplot2, HDF5Array, matrixStats, methods,
        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
biocViews: RNASeq, AlternativeSplicing, Sequencing, Software, Genetics,
        Coverage
URL: https://github.com/gagneurlab/FRASER
RoxygenNote: 7.1.0
Encoding: UTF-8
Collate: variables.R getNSetterFuns.R FRASER-package.R
        FraserDataSet-class.R AllGenerics.R Fraser-pipeline.R
        accessor-methods.R annotationOfRanges.R beta-binomial-testing.R
        calculatePSIValue.R calculateStats.R countRNAseqData.R
        example_functions.R filterExpression.R
        find_encoding_dimensions.R getURLs.R helper-functions.R
        saveHDF5Objects.R RcppExports.R autoencoder.R updateD.R
        updateE.R updateRho.R pvalsNzscore.R makeSimulatedDataset.R
        fitCorrectionMethods.R plotMethods.R zzz.R
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/FRASER
git_branch: RELEASE_3_11
git_last_commit: fd332b9
git_last_commit_date: 2020-06-08
Date/Publication: 2020-06-08
NeedsCompilation: yes
Packaged: 2020-06-09 04:42:42 UTC; biocbuild
Built: R 4.0.0; x86_64-apple-darwin13.4.0; 2020-06-12 02:26:14 UTC; unix
