Man pages for tgirke/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
createWFConstructs SYSargs2 object and creates CWL param files
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"'
loadWorkflowConstructs SYSargs2 object from CWL param and targets files
mergeBamByFactorMerge BAM files based on factor
moduleInterface to allow full use of the Environment Modules system...
moduleloadInterface to module system
olBarplotBar plot for intersect sets
olRangesIdentify Range Overlaps for IRanges and GRanges Object
output_updateUpdates the output files paths in the 'SYSargs2' object
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
renderWFPopulate all the command-line in an 'SYSargs2' object
returnRPKMRPKM Normalization
runCommandlineExecute SYSargs and SYSargs2
run_DESeq2Runs DESeq2
runDiffDifferential abundance analysis for many range sets
run_edgeRRuns edgeR
run_trackKeep track of the all 'SYSargs2' object
scaleRangesScale spliced ranges to genome coordinates
seeFastqQuality reports for FASTQ files
subsetWFSubsetting SYSargs2 class slots
symLink2bamSymbolic links for IGV
sysargsSYSargs accessor methods
SYSargs2-classClass '"SYSargs2"'
SYSargs2list-methodsSYSargs2 accessor methods
SYSargs2Pipe-classClass '"SYSargs2Pipe"'
SYSargs2Pipe-methodsSYSargs2Pipe accessor methods
SYSargs-classClass '"SYSargs"'
systemArgsConstructs SYSargs object from param and targets files
targets.as.dfConvert targets list to data.frame
variantReportGenerate Variant Report
vennPlotPlot 2-5 way Venn diagrams
VENNset-classClass '"VENNset"'
writeTargetsoutWrite updated targets out to file
writeTargetsRefGenerate targets file with reference
tgirke/systemPipeR documentation built on Nov. 8, 2019, 10:17 a.m.