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
config.paramAdding param file
configWFWorkflow Steps Selection
countRangesetRead counting for several range sets
createWFConstructs SYSargs2 object and creates CWL param files
EnvModules-classClass '"EnvModules"'
evalCodeToggles option 'eval' on the RMarkdown 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
initWFWorkflow Project Initiation
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
plotWFGraphviz Plot Workflow
predORFPredict ORFs
preprocessReadsRun custom read preprocessing functions
qsubRunSubmit command-line tools to cluster
readCompImport sample comparisons from targets file
renderReportRender RMarkdown Report
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_trackDeprecated 'run_track' functions
runWFExecute SYSargsList
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"'
sysargs2-methodsSYSargs2 accessor methods
SYSargs2Pipe-classDeprecated '"SYSargs2Pipe"' Class
SYSargs2Pipe-methodsDeprecated '"SYSargs2Pipe"' accessor methods
SYSargs-classClass '"SYSargs"'
SYSargsList-classClass '"SYSargsList"'
sysargslist-methodsSYSargsList accessor methods
systemArgsConstructs SYSargs object from param and targets files targets list to data.frame
tryCLCollect information about the third-party software
tryPathValidation of the files or directories
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. 26, 2021, 2 a.m.