Bioinformatics pipelines based on Rcwl


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Documentation for package ‘RcwlPipelines’ version 1.0.11

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RcwlPipelines-package RcwlPipelines
alignMerge DNASeq alignment, merge and markduplicates
BaseRecal Base quality recalibration
bcfview bcftools view
bgzip bgzip
blastn blastn
bowtie2 bowtie2
bowtie2_build bowtie2-build
bwa bwa mem
bwaAlign bwaAlign
bwaMMRecal DNASeq alignment, merge, markduplicates and recalibration
bwaMRecal DNASeq alignment, markduplicates and recalibration
bwa_index bwa index
CalculateContamination gatk CalculateContamination
ColSeqArtifact gatk CollectSequencingArtifactMetrics
cutadapt cutadapt
cwlTools cwlTools
fastqc fastqc
featureCounts featureCounts
FilterMutectCalls gatk FilterMutectCalls
FilterOBias gatk FilterByOrientationBias
Funcotator gatk Funcotator
GAlign GATK alignment pipeline
geneBody_coverage geneBody_coverage.py
genePredToBed genePredToBed
GenomicsDB gatk GenomicsDBImport
GetPileupSummaries gatk GetPileupSummaries
GPoN GATK4: create a panel of normals
gtfToGenePred gtfToGenePred
hapCall GATK haplotypecaller pipeline
hisat2_align hisat2
hisat2_build hisat2-build
htseq htseq-count
jdCall GATK joint discovery pipeline
lancet lancet
LoFreq LoFreq
makeblastdb makeblastdb
manta manta
mantaStrelka strelka somatic caller
markdup picard MarkDuplicates
mergeBam picard MergeSamFiles
mergeBamDup mergeBamDup
multiqc multiqc
MuSE MuSE
Mutect2 gatk Mutect2
Mutect2PL GATK4: Mutect2
mvOut Rscript: mvOut
neusomatic neusomatic caller
polysolver polysolver
PoN gatk CreateSomaticPanelOfNormals
RcwlPipelines RcwlPipelines
read_distribution read_distribution.py
rnaseq_Sf RNASeq pipeline with STAR and featureCounts
RSeQC RNASeq quality control by RSeQC
runWDL java: runWDL
salmon_index salmon index
salmon_quant salmon quant
sam2bam samtools view
samtools_flagstat samtools flagstat
samtools_index samtools index
samtools_mpileup samtools_mpileup
SomaticSniper SomaticSniper
sortBam samtools sort
STAR STAR
starFusion STAR-Fusion
strelka strelka
tabix_index tabix index
VarDict VarDict
VarScan2Somatic VarScan2 somatic caller
VarScan2_processSomatic VarScan2_processSomatic
VarScan2_somatic VarScan2_somatic
VarScan2_somaticFilter VarScan2_somaticFilter