Package: RcwlPipelines
Title: Bioinformatics pipelines based on Rcwl
Version: 1.2.0
Authors@R: 
    c(person(given = "Qiang", family = "Hu",
             role = c("aut", "cre"),
             email = "qiang.hu@roswellpark.org"),
      person(given = "Shuang", family = "Gao",
	     role = c("aut"),
	     email = "shuang.gao@roswellpark.org"))
Description: A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.
Depends: R (>= 3.6), Rcwl, BiocFileCache
Imports: dplyr, rappdirs, jsonlite, methods, utils, tximport
License: GPL-2
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
RoxygenNote: 6.1.1
biocViews: Software, WorkflowStep, Alignment, Preprocessing,
        QualityControl, DNASeq, RNASeq, DataImport, ImmunoOncology
SystemRequirements: nodejs
Collate: 'RcwlPipelines-package.R' 'cwlTools.R' 'doc_pipelines.R'
        'doc_tools.R' 'tl_tabix_index.R' 'tl_bgzip.R'
        'tl_ReadBackedPhasing.R' 'tl_SortVcf.R' 'tl_CombineVariants.R'
        'tl_RenameSampleInVcf.R' 'tl_bcfview.R' 'pl_phaseVcf.R'
        'tl_vcf_expression_annotator.R' 'tl_kallisto_quant.R'
        'pl_vcfExpression.R' 'tl_vcf_readcount_annotator.R'
        'tl_bam_readcount.R' 'tl_vt_decompose.R' 'pl_vcfCoverage.R'
        'tl_vep.R' 'pl_AnnPhaseVcf.R' 'tl_samtools_stats.R'
        'tl_samtools_flagstat.R' 'tl_samtools_index.R' 'tl_ApplyBQSR.R'
        'tl_BaseRecalibrator.R' 'pl_BaseRecal.R' 'tl_runWDL.R'
        'tl_mvOut.R' 'pl_GAlign.R' 'tl_PoN.R' 'tl_GenomicsDB.R'
        'pl_GPoN.R' 'tl_FilterOBias.R' 'tl_ColSeqArtifact.R'
        'tl_FilterMutectCalls.R' 'tl_CalculateContamination.R'
        'tl_GetPileupSummaries.R' 'tl_Mutect2.R' 'pl_Mutect2PL.R'
        'tl_geneBody_coverage.R' 'tl_read_distribution.R'
        'tl_genePredToBed.R' 'tl_gtfToGenePred.R' 'pl_RSeQC.R'
        'tl_neusomatic_postprocess.R' 'tl_neusomatic_call.R'
        'tl_neusomatic_preprocess.R' 'pl_neusomatic.R'
        'tl_SomaticSeq_Wrapper.R' 'tl_VarScan2_somaticFilter.R'
        'tl_VarScan2_processSomatic.R' 'tl_VarScan2_somatic.R'
        'tl_samtools_mpileup.R' 'pl_VarScan2Somatic.R' 'tl_LoFreq.R'
        'tl_VarDict.R' 'tl_SomaticSniper.R' 'tl_strelka.R' 'tl_manta.R'
        'pl_mantaStrelka.R' 'tl_MuSE.R' 'pl_SomaticCallers.R'
        'tl_markdup.R' 'tl_mergeBam.R' 'pl_mergeBamDup.R'
        'tl_sortBam.R' 'tl_sam2bam.R' 'tl_bwa.R' 'pl_bwaAlign.R'
        'pl_alignMerge.R' 'pl_bwaMMRecal.R' 'pl_bwaMRecal.R'
        'pl_hapCall.R' 'pl_jdCall.R' 'tl_miRDeep2.R' 'tl_miRMapper.R'
        'pl_miRDeep2PL.R' 'tl_featureCounts.R' 'tl_STAR.R'
        'tl_fastqc.R' 'pl_rnaseq_Sf.R' 'tl_BedToIntervalList.R'
        'tl_DepthOfCoverage.R' 'tl_Funcotator.R' 'tl_SamToFastq.R'
        'tl_VarScan2.R' 'tl_annovar.R' 'tl_blastn.R' 'tl_bowtie2.R'
        'tl_bowtie2_build.R' 'tl_bowtie_build.R' 'tl_bwa_index.R'
        'tl_cnvkit_batch.R' 'tl_cutadapt.R' 'tl_hisat2_align.R'
        'tl_hisat2_build.R' 'tl_htseq.R' 'tl_kallisto_index.R'
        'tl_lancet.R' 'tl_makeblastdb.R' 'tl_multiqc.R'
        'tl_polysolver.R' 'tl_pvacseq.R' 'tl_salmon_index.R'
        'tl_salmon_quant.R' 'tl_starFusion.R'
git_url: https://git.bioconductor.org/packages/RcwlPipelines
git_branch: RELEASE_3_10
git_last_commit: 5c395c4
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: no
Packaged: 2019-10-30 03:33:54 UTC; biocbuild
Author: Qiang Hu [aut, cre],
  Shuang Gao [aut]
Maintainer: Qiang Hu <qiang.hu@roswellpark.org>
