Package: HTSeqGenie
Imports: BiocGenerics (>= 0.2.0), IRanges (>= 1.14.3), GenomicRanges
        (>= 1.7.12), Rsamtools (>= 1.8.5), Biostrings (>= 2.24.1),
        chipseq (>= 1.6.1), rtracklayer (>= 1.17.19), GenomicFeatures
        (>= 1.9.31), VariantTools (>= 1.1.16), VariantAnnotation (>=
        1.5.41)
Maintainer: Gregoire Pau <pau.gregoire@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: 3.10.0
Date: 2012-03-01
Depends: R (>= 2.15.0), ShortRead (>= 1.14.4), parallel, hwriter,
        Cairo, tools, rtracklayer, gmapR (>= 1.1.10)
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, GenomicFeatures,
        LungCancerLines, org.Hs.eg.db
Collate: 'alignReads.R' 'bamUtils.R' 'checkConfig.R' 'config.R'
        'detectAdapterContam.R' 'detectRRNA.R' 'filterQuality.R' 'io.R'
        'preprocessReads.R' 'initPipeline.R' 'testHelpers.R' 'tools.R'
        'trimReads.R' 'zzz.R' 'countGenomicFeatures.R' 'coverage.R'
        'createSummaryCounts.R' 'mergeLanes.R' 'plotDepthByStrand.R'
        'readRNASeqEnds.R' 'reportPipelineQA.R' 'runPipeline.R'
        'targetLengths.R' 'summaries.R'
        'buildGenomicFeaturesFromTxDb.R' 'TP53GenomicFeatures.R'
        'wrapGsnap.R' 'picard.R' 'analyzeVariants.R' 'gatk.R'
        'logging.R'
Packaged: 2013-04-04 09:00:21 UTC; biocbuild
