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EnvModules-class [[,EnvModules,ANY,missing-method [[ [,EnvModules,ANY,ANY,ANY-method [[,EnvModules,ANY,ANY-method [[ [[ $,EnvModules-method available_modules,EnvModules-method coerce,EnvModules,list-method coerce,list,EnvModules-method default_modules,EnvModules-method EnvModules,EnvModules-method loaded_modules,EnvModules-method modulecmd,EnvModules-method names,EnvModules-method show,EnvModules-method
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Class "EnvModules" |
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makeCATdb() GOHyperGAll() GOHyperGAll_Subset() GOHyperGAll_Simplify() GOCluster_Report() goBarplot()
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GO term enrichment analysis for large numbers of gene sets |
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INTERSECTset-class as.list,INTERSECTset-method coerce,list,INTERSECTset-method complexitylevels,INTERSECTset-method intersectlist,INTERSECTset-method intersectmatrix,INTERSECTset-method length,INTERSECTset-method names,INTERSECTset-method setlist,INTERSECTset-method show,INTERSECTset-method
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Class "INTERSECTset" |
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LineWise()
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Class "LineWise" |
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printParam() subsetParam() replaceParam() renameParam() appendParam()
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Accessories function to modify the Command-line Version 1 |
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printParam2() appendParam2() replaceParam2() removeParam2() renameParam2()
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Accessories function to modify the Command-line Version 2 |
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SPRproject()
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Workflow Project Initiation |
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SYSargs-class [,SYSargs,ANY,ANY,ANY-method coerce,list,SYSargs-method cores,SYSargs-method infile1,SYSargs-method infile2,SYSargs-method modules,SYSargs-method names,SYSargs-method length,SYSargs-method other,SYSargs-method results,SYSargs-method outfile1,SYSargs-method outpaths,SYSargs-method reference,SYSargs-method show,SYSargs-method software,SYSargs-method sysargs,SYSargs-method SampleName,SYSargs-method targetsheader,SYSargs-method targetsin,SYSargs-method targetsout,SYSargs-method
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Class "SYSargs" |
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SYSargs2-class [,SYSargs2,ANY,ANY,ANY-method [[,SYSargs2,ANY,missing-method [[ [[ $,SYSargs2-method length,SYSargs2-method names,SYSargs2-method show,SYSargs2-method coerce,list,SYSargs2-method coerce,SYSargs2,list-method sysargs2 sysargs2,SYSargs2-method targets targets,SYSargs2-method targetsheader,SYSargs2-method modules modules,SYSargs2-method infile1,SYSargs2-method infile2,SYSargs2-method wf wf,SYSargs2-method clt clt,SYSargs2-method yamlinput,SYSargs2-method cmdlist,SYSargs2-method input input,SYSargs2-method output output,SYSargs2-method files files,SYSargs2-method inputvars inputvars,SYSargs2-method cmdToCwl cmdToCwl,SYSargs2-method status status,SYSargs2-method internal_outfiles internal_outfiles,SYSargs2-method baseCommand,SYSargs2-method SampleName,SYSargs2-method yamlinput yamlinput cmdToCwl cmdToCwl
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Class "SYSargs2" |
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stepsWF() statusWF() targetsWF() outfiles() SE() dependency() projectInfo() runInfo() cmdlist() codeLine() SampleName() stepName() baseCommand() targetsheader() yamlinput() viewEnvir() copyEnvir() addResources() subset() getColumn() `appendStep<-`() `yamlinput<-`() `replaceStep<-`() `renameStep<-`() `dependency<-`() `appendCodeLine<-`() `replaceCodeLine<-`() `updateColumn<-`()
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Class "SYSargsList" |
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SYSargsList()
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SYSargsList Constructor |
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VENNset-class as.list,VENNset-method coerce,list,VENNset-method complexitylevels,VENNset-method intersectmatrix,VENNset-method length,VENNset-method names,VENNset-method setlist,VENNset-method show,VENNset-method vennlist,VENNset-method
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Class "VENNset" |
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addAssay() addMetadata()
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Extension accessor methods for SummarizedExperiment object |
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alignStats()
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Alignment statistics |
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catDB-class catlist,catDB-method catmap,catDB-method coerce,list,catDB-method idconv,catDB-method names,catDB-method show,catDB-method
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Class "catDB" |
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catmap()
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catDB accessor methods |
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check.output() check.outfiles()
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Checking if the outfiles files exist |
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clusterRun()
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Submit command-line tools to cluster |
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config.param()
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Adding param file |
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configWF()
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Workflow Steps Selection |
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countRangeset()
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Read counting for several range sets |
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createParamFiles() writeParamFiles()
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createParam |
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cwlFilesUpdate()
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Update CWL description files |
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evalCode()
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Toggles option eval on the RMarkdown files |
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featureCoverage()
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Genome read coverage by transcript models |
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featuretypeCounts()
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Plot read distribution across genomic features |
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filterDEGs()
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Filter and plot DEG results |
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filterVars()
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Filter VCF files |
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genFeatures()
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Generate feature ranges from TxDb |
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importWF()
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Import R Markdown file as workflow |
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listCmdTools() listCmdModules()
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List/check the existence of command-line tools of a workflow |
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loadWorkflow() renderWF() updateWF()
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Constructs SYSargs2 object from CWL param and targets files |
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mergeBamByFactor()
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Merge BAM files based on factor |
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module() moduleload() moduleUnload() modulelist() moduleAvail() moduleClear() moduleInit()
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Interface to allow full use of the Environment Modules system for Unix |
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olBarplot()
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Bar plot for intersect sets |
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olRanges()
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Identify Range Overlaps for IRanges and GRanges Object |
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output_update()
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Updates the output files paths in the SYSargs2 object |
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overLapper()
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Set Intersect and Venn Diagram Functions |
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plotWF() plotwfOutput() renderPlotwf()
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Visualize SPR workflow and status |
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plotfeatureCoverage()
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Plot feature coverage results |
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plotfeaturetypeCounts()
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Plot read distribution across genomic features |
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predORF()
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Predict ORFs |
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preprocessReads()
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Run custom read preprocessing functions |
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readComp()
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Import sample comparisons from targets file |
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renderLogs()
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Render RMarkdown Logs Report |
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renderReport()
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Render RMarkdown Report |
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returnRPKM()
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RPKM Normalization |
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runCommandline()
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Execute SYSargs and SYSargs2 |
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runDiff()
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Differential abundance analysis for many range sets |
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runWF()
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Execute SYSargsList |
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run_DESeq2()
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Runs DESeq2 |
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run_edgeR()
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Runs edgeR |
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sal2bash()
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Translate SYSargsList back to a bash workflow |
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sal2rmd()
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Translate SYSargsList back to a workflow template Rmarkdown file |
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scaleRanges()
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Scale spliced ranges to genome coordinates |
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seeFastq() seeFastqPlot()
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Quality reports for FASTQ files |
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showDF()
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Create an HTML table using DT package with fixed columns |
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subsetWF()
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Subsetting SYSargs2 class slots |
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symLink2bam()
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Symbolic links for IGV |
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sysargs()
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SYSargs accessor methods |
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systemArgs()
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Constructs SYSargs object from param and targets files |
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systemPipeR-package
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systemPipeR package for Workflow Environment |
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targets.as.df() targets.as.list()
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Convert targets to list or data.frame |
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trimbatch()
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Genome read coverage by transcript models |
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tryCMD()
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Collect information about the third-party software |
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tryPath()
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Validation of the files or directories |
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variantReport() combineVarReports() varSummary()
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Generate Variant Report |
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vennPlot()
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Plot 2-5 way Venn diagrams |
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writeTargets()
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Write updated targets out to file from SYSargsList |
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writeTargetsRef()
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Generate targets file with reference |
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writeTargetsout()
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Write updated targets out to file |
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write_SYSargsList()
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Writeout SYSargsList object |