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

add-methodsExtension accessor methods for SummarizedExperiment object
alignStatsAlignment statistics
catDB-classClass '"catDB"'
catmapcatDB accessor methods
check.outputChecking if the outfiles files exist
clusterRunSubmit command-line tools to cluster
config.paramAdding param file
configWFWorkflow Steps Selection
countRangesetRead counting for several range sets
createParamFilescreateParam
cwlFilesUpdateUpdate CWL description 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
GOHyperGAllGO term enrichment analysis for large numbers of gene sets
importWFImport R Markdown file as workflow
INTERSECTset-classClass '"INTERSECTset"'
LineWise-classClass '"LineWise"'
loadWorkflowConstructs SYSargs2 object from CWL param and targets files
mergeBamByFactorMerge BAM files based on factor
moduleloadInterface to allow full use of the Environment Modules 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
ParamFilesAccessories function to modify the Command-line Version 1
ParamFiles2Accessories function to modify the Command-line Version 2
plotfeatureCoveragePlot feature coverage results
plotfeaturetypeCountsPlot read distribution across genomic features
plotWFVisualize SPR workflow and status
predORFPredict ORFs
preprocessReadsRun custom read preprocessing functions
readCompImport sample comparisons from targets file
renderLogsRender RMarkdown Logs Report
renderReportRender RMarkdown Report
returnRPKMRPKM Normalization
runCommandlineExecute SYSargs and SYSargs2
run_DESeq2Runs DESeq2
runDiffDifferential abundance analysis for many range sets
run_edgeRRuns edgeR
runWFExecute SYSargsList
sal2bashTranslate SYSargsList back to a bash workflow
sal2rmdTranslate SYSargsList back to a workflow template Rmarkdown...
scaleRangesScale spliced ranges to genome coordinates
seeFastqQuality reports for FASTQ files
showDFCreate an HTML table using DT package with fixed columns
SPRprojectWorkflow Project Initiation
subsetWFSubsetting SYSargs2 class slots
symLink2bamSymbolic links for IGV
sysargsSYSargs accessor methods
SYSargs2-classClass '"SYSargs2"'
SYSargs-classClass '"SYSargs"'
SYSargsListSYSargsList Constructor
SYSargsList-classClass '"SYSargsList"'
systemArgsConstructs SYSargs object from param and targets files
systemPipeR-packagesystemPipeR package for Workflow Environment
targets.as.dfConvert targets to list or data.frame
trimbatchGenome read coverage by transcript models
tryCMDCollect information about the third-party software
tryPathValidation of the files or directories
variantReportGenerate Variant Report
vennPlotPlot 2-5 way Venn diagrams
VENNset-classClass '"VENNset"'
write_SYSargsListWriteout SYSargsList object
writeTargetsWrite updated targets out to file from 'SYSargsList'
writeTargetsoutWrite updated targets out to file
writeTargetsRefGenerate targets file with reference
tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.