HTSeqGenie

Package: HTSeqGenie
Imports: BiocGenerics (>= 0.2.0), S4Vectors (>= 0.9.25), IRanges (>=
1.21.39), GenomicRanges (>= 1.23.21), Rsamtools (>= 1.8.5),
Biostrings (>= 2.24.1), chipseq (>= 1.6.1), hwriter (>= 1.3.0),
Cairo (>= 1.5.5), GenomicFeatures (>= 1.9.31), BiocParallel,
parallel, tools, rtracklayer (>= 1.17.19), GenomicAlignments,
VariantTools (>= 1.7.7), GenomeInfoDb, SummarizedExperiment,
methods
Maintainer: Jens Reeder <reeder.jens@gene.com>
License: Artistic-2.0
Title: A NGS analysis pipeline.
Type: Package
LazyLoad: yes
Author: Gregoire Pau, Jens Reeder
Description: Libraries to perform NGS analysis.
Version: 4.2.0
Depends: R (>= 3.0.0), gmapR (>= 1.8.0), ShortRead (>= 1.19.13),
VariantAnnotation (>= 1.8.3)
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines,
org.Hs.eg.db
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 04:46:04 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'HTSeqGenie' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'HTSeqGenie'
    finding HTML links ... done
    FastQStreamer.getReads                  html  
    FastQStreamer.init                      html  
    FastQStreamer.release                   html  
    HTSeqGenie                              html  
    TP53GenomicFeatures                     html  
    alignReads                              html  
    alignReadsChunk                         html  
    analyzeVariants                         html  
    bamCountUniqueReads                     html  
    buildConfig                             html  
    buildGenomicFeaturesFromTxDb            html  
    buildShortReadReports                   html  
    buildTP53FastaGenome                    html  
    buildTP53GenomeTemplate                 html  
    buildTallyParam                         html  
    calculateCoverage                       html  
    calculateTargetLengths                  html  
    callVariantsGATK                        html  
    checkConfig                             html  
    checkGATKJar                            html  
    checkPicardJar                          html  
    computeBamStats                         html  
    computeCoverage                         html  
    countFeatures                           html  
    countGenomicFeatures                    html  
    countGenomicFeaturesChunk               html  
    createTmpDir                            html  
    detectAdapterContam                     html  
    detectQualityInFASTQFile                html  
    detectRRNA                              html  
    excludeVariantsByRegions                html  
    filterByLength                          html  
    filterQuality                           html  
    findVariantFile                         html  
    gatk                                    html  
    generateSingleGeneDERs                  html  
    getAdapterSeqs                          html  
    getBams                                 html  
    getChunkDirs                            html  
    getConfig                               html  
    getConfig.integer                       html  
    getConfig.logical                       html  
    getConfig.numeric                       html  
    getConfig.vector                        html  
    getEndNumber                            html  
    getMemoryUsage                          html  
    getNumberOfReadsInFASTQFile             html  
    getNumericVectorDataFromFile            html  
    getObjectFilename                       html  
    getPackageFile                          html  
    getRRNAIds                              html  
    getRandomAlignCutoff                    html  
    getTabDataFromFile                      html  
    getTraceback                            html  
    hashCoverage                            html  
    hashVariants                            html  
    hashVector                              html  
    initDirs                                html  
    initLog                                 html  
    initLogger                              html  
    initPipelineFromConfig                  html  
    initPipelineFromSaveDir                 html  
    isAboveQualityThresh                    html  
    isAdapter                               html  
    isConfig                                html  
    isFirstFragment                         html  
    isSparse                                html  
    listIterator.init                       html  
    listIterator.next                       html  
    loadConfig                              html  
    logdebug                                html  
    logerror                                html  
    loginfo                                 html  
    logwarn                                 html  
    makeDir                                 html  
    makeRandomSreads                        html  
    markDuplicates                          html  
    markDups                                html  
    mergeAlignReads                         html  
    mergeCoverage                           html  
    mergeLanes                              html  
    mergePreprocessReads                    html  
    mergeSummaryAlignment                   html  
    parseDCF                                html  
    parseSummaries                          html  
    picard                                  html  
    plotDF                                  html  
    preprocessReads                         html  
    preprocessReadsChunk                    html  
    processChunks                           html  
    readInputFiles                          html  
    readRNASeqEnds                          html  
    realignIndels                           html  
    realignIndelsGATK                       html  
    relativeBarPlot                         html  
    removeChunkDir                          html  
    resource                                html  
    rpkm                                    html  
    runAlignment                            html  
    runPipeline                             html  
    runPipelineConfig                       html  
    runPreprocessReads                      html  
    safe.yield                              html  
    safeExecute                             html  
    safeGetObject                           html  
    safeUnlink                              html  
    saveWithID                              html  
    sclapply                                html  
    setChunkDir                             html  
    setUpDirs                               html  
    setupTestFramework                      html  
    statCountFeatures                       html  
    traceMem                                html  
    trimReads                               html  
    trimTailsByQuality                      html  
    truncateReads                           html  
    tryKeepTraceback                        html  
    updateConfig                            html  
    vcfStat                                 html  
    wrap.callVariants                       html  
    writeAudit                              html  
    writeConfig                             html  
    writeFastQFiles                         html  
    writeFeatureCountsHTML                  html  
    writeGenomicFeaturesReport              html  
    writePreprocessAlignHTML                html  
    writePreprocessAlignReport              html  
    writeSummary                            html  
    writeVCF                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HTSeqGenie)
Making 'packages.html' ... done