Man pages for systemPipeR
systemPipeR: NGS workflow and report generation environment

alignStatsAlignment statistics
catDB-classClass '"catDB"'
catmapcatDB accessor methods
clusterRunSubmit command-line tools to cluster
countRangesetRead counting for several range sets
featureCoverageGenome read coverage by transcript models
featuretypeCountsPlot read distribution across genomic features
filterDEGsFilter and plot DEG results
filterVarsFilter VCF files
genFeaturesGenerate feature ranges from TxDb
getQsubargsArguments for qsub
GOHyperGAllGO term enrichment analysis for large numbers of gene sets
INTERSECTset-classClass '"INTERSECTset"'
mergeBamByFactorMerge BAM files based on factor
moduleloadInterface to module system
olBarplotBar plot for intersect sets
overLapperSet Intersect and Venn Diagram Functions
plotfeatureCoveragePlot feature coverage results
plotfeaturetypeCountsPlot read distribution across genomic features
predORFPredict ORFs
preprocessReadsRun custom read preprocessing functions
qsubRunSubmit command-line tools to cluster
readCompImport sample comparisons from targets file
returnRPKMRPKM Normalization
runCommandlineExecute SYSargs
run_DESeq2Runs DESeq2
runDiffDifferential abundance analysis for many range sets
run_edgeRRuns edgeR
scaleRangesScale spliced ranges to genome coordinates
seeFastqQuality reports for FASTQ files
symLink2bamSymbolic links for IGV
sysargsSYSargs accessor methods
SYSargs-classClass '"SYSargs"'
systemArgsConstructs SYSargs object from param and targets files
variantReportGenerate Variant Report
vennPlotPlot 2-5 way Venn diagrams
VENNset-classClass '"VENNset"'
writeTargetsoutWrite updated targets out to file
writeTargetsRefGenerate targets file with reference
systemPipeR documentation built on Jan. 5, 2019, 7 p.m.