| $,EnvModules-method |
Man page
|
| $,LineWise-method |
Man page
|
| $,SYSargs2-method |
Man page
|
| $,SYSargsList-method |
Man page
|
| .AffyID2GeneID |
Source code
|
| .StepClass |
Source code
|
| .WFcompact |
Source code
|
| .WFhori |
Source code
|
| .WFlinear |
Source code
|
| .WFvert |
Source code
|
| .addDotLegend |
Source code
|
| .addDotLegendUri |
Source code
|
| .addNodeDecor |
Source code
|
| .allAnnot |
Source code
|
| .bashRStep |
Source code
|
| .bashSysStep |
Source code
|
| .buildDF |
Source code
|
| .buildInlist2 |
Source code
|
| .buildTree |
Source code
|
| .catArgs2 |
Source code
|
| .catBase |
Source code
|
| .catBase2 |
Source code
|
| .catCmdAll2 |
Source code
|
| .catCmdRaw |
Source code
|
| .catCmdRaw2 |
Source code
|
| .catInputs |
Source code
|
| .catInputs2 |
Source code
|
| .catOutputs |
Source code
|
| .catOutputs2 |
Source code
|
| .catStdout2 |
Source code
|
| .cbindTargetsOutfiles |
Source code
|
| .check.output.sysargs2 |
Source code
|
| .checkInlist2 |
Source code
|
| .checkInputVars |
Source code
|
| .checkInstr2 |
Source code
|
| .checkOutArgs2 |
Source code
|
| .check_write_SYSargsList |
Source code
|
| .cmd2cwl2 |
Source code
|
| .cmdAppend2 |
Source code
|
| .cmdRemove2 |
Source code
|
| .cmdRename2 |
Source code
|
| .cmdReplace2 |
Source code
|
| .cmdToCwl |
Source code
|
| .codingReport |
Source code
|
| .collapseSteps |
Source code
|
| .cwlAppend |
Source code
|
| .cwlIndexTrim |
Source code
|
| .cwlRename |
Source code
|
| .cwlReplace |
Source code
|
| .findBranch |
Source code
|
| .gene2GOlist |
Source code
|
| .getAllCmdNames2 |
Source code
|
| .getPreprotext |
Source code
|
| .getSRAfastq |
Source code
|
| .makeBam |
Source code
|
| .modifyCwlParse |
Source code
|
| .moduleload |
Source code
|
| .parseInStr |
Source code
|
| .parseInstr2 |
Source code
|
| .parseNewIn |
Source code
|
| .parseNewOut |
Source code
|
| .parseOutStr |
Source code
|
| .readGOorg |
Source code
|
| .recommendBranch |
Source code
|
| .removeSpaces2 |
Source code
|
| .renderMsg |
Source code
|
| .renderWFsingle |
Source code
|
| .resizeFeature |
Source code
|
| .sal2rmd_rstep |
Source code
|
| .sal2rmd_sysstep |
Source code
|
| .sampleDFgene2GO |
Source code
|
| .showHelper |
Source code
|
| .stepDuration |
Source code
|
| .subsetReadsByMappingRegion |
Source code
|
| .sysargsrunCommandline |
Source code
|
| .tryRunC |
Source code
|
| .validationStepConn |
Source code
|
| .writeRscript |
Source code
|
| EnvModules,EnvModules-method |
Man page
|
| EnvModules-class |
Man page
|
| GOCluster_Report |
Man page
Source code
|
| GOHyperGAll |
Man page
Source code
|
| GOHyperGAll_Simplify |
Man page
Source code
|
| GOHyperGAll_Subset |
Man page
Source code
|
| INTERSECTset-class |
Man page
|
| LineWise |
Man page
Source code
|
| LineWise-class |
Man page
|
| SE |
Man page
|
| SE,SYSargsList-method |
Man page
|
| SE<- |
Man page
|
| SE<-,SYSargsList-method |
Man page
|
| SPRdata |
Source code
|
| SPRproject |
Man page
Source code
|
| SYSargs-class |
Man page
|
| SYSargs2-class |
Man page
|
| SYSargsList |
Man page
Source code
|
| SYSargsList-class |
Man page
|
| SampleName |
Man page
Man page
|
| SampleName,SYSargs-method |
Man page
|
| SampleName,SYSargs2-method |
Man page
|
| SampleName,SYSargsList-method |
Man page
|
| SampleName-methods |
Man page
|
| VENNset-class |
Man page
|
| [,EnvModules,ANY,ANY,ANY-method |
Man page
|
| [,LineWise,ANY,ANY,ANY-method |
Man page
|
| [,SYSargs,ANY,ANY,ANY-method |
Man page
|
| [,SYSargs2,ANY,ANY,ANY-method |
Man page
|
| [,SYSargsList,ANY,ANY,ANY-method |
Man page
|
| [[,EnvModules,ANY,ANY-method |
Man page
|
| [[,EnvModules,ANY,missing-method |
Man page
|
| [[,LineWise,ANY,missing-method |
Man page
|
| [[,SYSargs2,ANY,missing-method |
Man page
|
| [[,SYSargsList,ANY,missing-method |
Man page
|
| [[<-,EnvModules,ANY,ANY,ANY-method |
Man page
|
| [[<-,EnvModules,ANY,ANY-method |
Man page
|
| [[<-,EnvModules-method |
Man page
|
| [[<-,LineWise,ANY,ANY,ANY-method |
Man page
|
| [[<-,LineWise,ANY,ANY-method |
Man page
|
| [[<-,SYSargs2,ANY,ANY,ANY-method |
Man page
|
| [[<-,SYSargs2,ANY,ANY-method |
Man page
|
| [[<-,SYSargsList,ANY,ANY,ANY-method |
Man page
|
| [[<-,SYSargsList,ANY,ANY-method |
Man page
|
| `+.SYSargsList` |
Source code
|
| addAssay |
Man page
|
| addAssay,SummarizedExperiment-method |
Man page
|
| addAssay-methods |
Man page
|
| addMetadata |
Man page
|
| addMetadata,SummarizedExperiment-method |
Man page
|
| addMetadata-methods |
Man page
|
| addResources |
Man page
|
| addResources,SYSargsList-method |
Man page
|
| alignStats |
Man page
Source code
|
| appendCodeLine,LineWise-method |
Man page
|
| appendCodeLine<- |
Man page
Man page
|
| appendCodeLine<-,LineWise,ANY,ANY,ANY-method |
Man page
|
| appendCodeLine<-,LineWise-method |
Man page
|
| appendCodeLine<-,SYSargsList-method |
Man page
|
| appendParam |
Man page
Source code
|
| appendParam2 |
Man page
Source code
|
| appendStep<- |
Man page
|
| appendStep<-,SYSargsList-method |
Man page
|
| as.list,INTERSECTset-method |
Man page
|
| as.list,VENNset-method |
Man page
|
| assembleCommandlineList |
Source code
|
| available_modules,EnvModules-method |
Man page
|
| baseCommand |
Man page
Man page
|
| baseCommand,SYSargs2-method |
Man page
|
| baseCommand,SYSargsList-method |
Man page
|
| catDB-class |
Man page
|
| catlist |
Man page
|
| catlist,catDB-method |
Man page
|
| catlist-methods |
Man page
|
| catmap |
Man page
|
| catmap,catDB-method |
Man page
|
| catmap-methods |
Man page
|
| check.outfiles |
Man page
|
| check.output |
Man page
Source code
|
| checkPkg |
Source code
|
| clt |
Man page
|
| clt,SYSargs2-method |
Man page
|
| clusterRCode |
Source code
|
| clusterRun |
Man page
Source code
|
| cmdToCwl |
Man page
|
| cmdToCwl,SYSargs2-method |
Man page
|
| cmdToCwl<- |
Man page
|
| cmdToCwl<-,SYSargs2-method |
Man page
|
| cmdTool2wf |
Source code
|
| cmdlist |
Man page
Man page
|
| cmdlist,SYSargs2-method |
Man page
|
| cmdlist,SYSargsList-method |
Man page
|
| codeChunkStart |
Man page
|
| codeChunkStart,LineWise-method |
Man page
|
| codeLine |
Man page
|
| codeLine,LineWise-method |
Man page
|
| codeLine,SYSargsList-method |
Man page
|
| coerce,EnvModules,list-method |
Man page
|
| coerce,LineWise,list-method |
Man page
|
| coerce,SYSargs2,list-method |
Man page
|
| coerce,SYSargsList,list-method |
Man page
|
| coerce,list,EnvModules-method |
Man page
|
| coerce,list,INTERSECTset-method |
Man page
|
| coerce,list,LineWise-method |
Man page
|
| coerce,list,SYSargs-method |
Man page
|
| coerce,list,SYSargs2-method |
Man page
|
| coerce,list,SYSargsList-method |
Man page
|
| coerce,list,VENNset-method |
Man page
|
| coerce,list,catDB-method |
Man page
|
| combineVarReports |
Man page
Source code
|
| complexitylevels |
Man page
|
| complexitylevels,INTERSECTset-method |
Man page
|
| complexitylevels,VENNset-method |
Man page
|
| complexitylevels-methods |
Man page
|
| config.param |
Man page
|
| configWF |
Man page
Source code
|
| copyEnvir |
Man page
|
| copyEnvir,SYSargsList-method |
Man page
|
| cores |
Man page
|
| cores,SYSargs-method |
Man page
|
| cores-methods |
Man page
|
| countRangeset |
Man page
Source code
|
| createParam |
Man page
|
| createParamFiles |
Man page
Source code
|
| createWF |
Source code
|
| cwlFilesUpdate |
Man page
|
| default_modules,EnvModules-method |
Man page
|
| dependency |
Man page
|
| dependency,LineWise-method |
Man page
|
| dependency,SYSargsList-method |
Man page
|
| dependency<- |
Man page
|
| dependency<-,SYSargsList-method |
Man page
|
| evalCode |
Man page
|
| featureCoverage |
Man page
Source code
|
| featuretypeCounts |
Man page
Source code
|
| files |
Man page
|
| files,LineWise-method |
Man page
|
| files,SYSargs2-method |
Man page
|
| filterDEGs |
Man page
Source code
|
| filterVars |
Man page
Source code
|
| findBestMatch |
Source code
|
| genFeatures |
Man page
Source code
|
| getColumn |
Man page
|
| getColumn,SYSargsList-method |
Man page
|
| goBarplot |
Man page
Source code
|
| idconv |
Man page
|
| idconv,catDB-method |
Man page
|
| idconv-methods |
Man page
|
| importWF |
Man page
Source code
|
| infile1 |
Man page
|
| infile1,SYSargs-method |
Man page
|
| infile1,SYSargs2-method |
Man page
|
| infile1-methods |
Man page
|
| infile2 |
Man page
|
| infile2,SYSargs-method |
Man page
|
| infile2,SYSargs2-method |
Man page
|
| infile2-methods |
Man page
|
| injectCommandlinelist |
Source code
|
| injectListbyName |
Source code
|
| input |
Man page
|
| input,SYSargs2-method |
Man page
|
| inputvars |
Man page
|
| inputvars,SYSargs2-method |
Man page
|
| internal_outfiles |
Man page
|
| internal_outfiles,SYSargs2-method |
Man page
|
| intersectlist |
Man page
|
| intersectlist,INTERSECTset-method |
Man page
|
| intersectlist-methods |
Man page
|
| intersectmatrix |
Man page
|
| intersectmatrix,INTERSECTset-method |
Man page
|
| intersectmatrix,VENNset-method |
Man page
|
| intersectmatrix-methods |
Man page
|
| is.modules.avail |
Source code
|
| length,INTERSECTset-method |
Man page
|
| length,LineWise-method |
Man page
|
| length,SYSargs-method |
Man page
|
| length,SYSargs2-method |
Man page
|
| length,SYSargsList-method |
Man page
|
| length,VENNset-method |
Man page
|
| linewise |
Man page
|
| linewise,LineWise-method |
Man page
|
| listCmdModules |
Man page
|
| listCmdTools |
Man page
|
| loadWF |
Man page
|
| loadWorkflow |
Man page
Source code
|
| loaded_modules,EnvModules-method |
Man page
|
| makeCATdb |
Man page
Source code
|
| makeDot |
Source code
|
| mergeBamByFactor |
Man page
Source code
|
| module |
Man page
Source code
|
| module.Clear.Init |
Source code
|
| module.List.Avail |
Source code
|
| module.Load.Unload |
Source code
|
| moduleAvail |
Man page
Source code
|
| moduleClear |
Man page
Source code
|
| moduleInit |
Man page
Source code
|
| moduleUnload |
Man page
Source code
|
| modulecmd,EnvModules-method |
Man page
|
| modulelist |
Man page
Source code
|
| moduleload |
Man page
Source code
|
| modules |
Man page
|
| modules,SYSargs-method |
Man page
|
| modules,SYSargs2-method |
Man page
|
| modules-methods |
Man page
|
| myEnvModules |
Source code
|
| nameUnnamed |
Source code
|
| names,EnvModules-method |
Man page
|
| names,INTERSECTset-method |
Man page
|
| names,LineWise-method |
Man page
|
| names,SYSargs-method |
Man page
|
| names,SYSargs2-method |
Man page
|
| names,SYSargsList-method |
Man page
|
| names,VENNset-method |
Man page
|
| names,catDB-method |
Man page
|
| nestedNames |
Source code
|
| olBarplot |
Man page
Source code
|
| olRanges |
Man page
Source code
|
| other |
Man page
|
| other,SYSargs-method |
Man page
|
| other-methods |
Man page
|
| outfile1 |
Man page
|
| outfile1,SYSargs-method |
Man page
|
| outfile1-methods |
Man page
|
| outfiles |
Man page
|
| outfiles,SYSargsList-method |
Man page
|
| outpaths |
Man page
|
| outpaths,SYSargs-method |
Man page
|
| outpaths-methods |
Man page
|
| output |
Man page
|
| output,SYSargs2-method |
Man page
|
| output.as.df |
Source code
|
| output_update |
Man page
Source code
|
| overLapper |
Man page
Source code
|
| parseRmd |
Source code
|
| pathInstance |
Source code
|
| pathUtils |
Source code
|
| plotWF |
Man page
Source code
|
| plotfeatureCoverage |
Man page
Source code
|
| plotfeaturetypeCounts |
Man page
Source code
|
| plotwfOutput |
Man page
Source code
|
| populateCommandline |
Source code
|
| predORF |
Man page
Source code
|
| preprocessReads |
Man page
Source code
|
| printParam |
Man page
Source code
|
| printParam2 |
Man page
Source code
|
| projectInfo |
Man page
|
| projectInfo,SYSargsList-method |
Man page
|
| readComp |
Man page
Source code
|
| readSE |
Source code
|
| read_SYSargsList |
Source code
|
| reference |
Man page
|
| reference,SYSargs-method |
Man page
|
| reference-methods |
Man page
|
| removeParam2 |
Man page
Source code
|
| renameParam |
Man page
Source code
|
| renameParam2 |
Man page
Source code
|
| renameStep<- |
Man page
|
| renameStep<-,SYSargsList-method |
Man page
|
| renderCommandline |
Source code
|
| renderInputs |
Source code
|
| renderLogs |
Man page
Source code
|
| renderOutputs |
Source code
|
| renderPlotwf |
Man page
Source code
|
| renderReport |
Man page
Source code
|
| renderWF |
Man page
Source code
|
| replaceCodeLine,LineWise-method |
Man page
|
| replaceCodeLine<- |
Man page
Man page
|
| replaceCodeLine<-,LineWise,ANY,ANY,ANY-method |
Man page
|
| replaceCodeLine<-,LineWise-method |
Man page
|
| replaceCodeLine<-,SYSargsList-method |
Man page
|
| replaceParam |
Man page
Source code
|
| replaceParam2 |
Man page
Source code
|
| replaceStep<- |
Man page
|
| replaceStep<-,SYSargsList-method |
Man page
|
| results |
Man page
|
| results,SYSargs-method |
Man page
|
| results-methods |
Man page
|
| returnRPKM |
Man page
Source code
|
| rmdPath |
Man page
|
| rmdPath,LineWise-method |
Man page
|
| runCommandline |
Man page
Source code
|
| runDiff |
Man page
Source code
|
| runInfo |
Man page
|
| runInfo,LineWise-method |
Man page
|
| runInfo,SYSargsList-method |
Man page
|
| runRcode |
Source code
|
| runWF |
Man page
Source code
|
| run_DESeq2 |
Man page
Source code
|
| run_edgeR |
Man page
Source code
|
| sal2bash |
Man page
Source code
|
| sal2rmd |
Man page
Source code
|
| scaleRanges |
Man page
Source code
|
| seeFastq |
Man page
Source code
|
| seeFastqPlot |
Man page
Source code
|
| setlist |
Man page
|
| setlist,INTERSECTset-method |
Man page
|
| setlist,VENNset-method |
Man page
|
| setlist-methods |
Man page
|
| show,EnvModules-method |
Man page
|
| show,INTERSECTset-method |
Man page
|
| show,LineWise-method |
Man page
|
| show,SYSargs-method |
Man page
|
| show,SYSargs2-method |
Man page
|
| show,SYSargsList-method |
Man page
|
| show,VENNset-method |
Man page
|
| show,catDB-method |
Man page
|
| showDF |
Man page
Source code
|
| software |
Man page
|
| software,SYSargs-method |
Man page
|
| software-methods |
Man page
|
| status |
Man page
|
| status,LineWise-method |
Man page
|
| status,SYSargs2-method |
Man page
|
| statusWF |
Man page
|
| statusWF,SYSargsList-method |
Man page
|
| status_color |
Source code
|
| stepName |
Man page
|
| stepName,LineWise-method |
Man page
|
| stepName,SYSargsList-method |
Man page
|
| stepsWF |
Man page
|
| stepsWF,SYSargsList-method |
Man page
|
| subset |
Man page
|
| subset,SYSargsList-method |
Man page
|
| subsetListbyName |
Source code
|
| subsetParam |
Man page
Source code
|
| subsetRmd |
Source code
|
| subsetWF |
Man page
Source code
|
| symLink2bam |
Man page
Source code
|
| sysargs |
Man page
|
| sysargs,SYSargs-method |
Man page
|
| sysargs-methods |
Man page
|
| sysargs2 |
Man page
|
| sysargs2,SYSargs2-method |
Man page
|
| sysargslist |
Man page
|
| sysargslist,SYSargsList-method |
Man page
|
| systemArgs |
Man page
Source code
|
| systemPipeR-package |
Man page
|
| targets |
Man page
|
| targets,SYSargs2-method |
Man page
|
| targets.as.df |
Man page
Source code
|
| targets.as.list |
Man page
Source code
|
| targetsWF |
Man page
|
| targetsWF,SYSargsList-method |
Man page
|
| targets_connection |
Man page
|
| targets_connection,SYSargsList-method |
Man page
|
| targetsheader |
Man page
Man page
|
| targetsheader,SYSargs-method |
Man page
|
| targetsheader,SYSargs2-method |
Man page
|
| targetsheader,SYSargsList-method |
Man page
|
| targetsheader-methods |
Man page
|
| targetsin |
Man page
|
| targetsin,SYSargs-method |
Man page
|
| targetsin-methods |
Man page
|
| targetsout |
Man page
|
| targetsout,SYSargs-method |
Man page
|
| targetsout-methods |
Man page
|
| termMMatch |
Source code
|
| trimbatch |
Man page
Source code
|
| tryCL |
Man page
|
| tryCMD |
Man page
|
| tryPath |
Man page
|
| updateColumn<- |
Man page
|
| updateColumn<-,SYSargsList-method |
Man page
|
| updateRmdTemplate |
Source code
|
| updateWF |
Man page
Source code
|
| varSummary |
Man page
Source code
|
| variantReport |
Man page
Source code
|
| vennPlot |
Man page
Source code
|
| vennlist |
Man page
|
| vennlist,VENNset-method |
Man page
|
| vennlist-methods |
Man page
|
| viewEnvir |
Man page
|
| viewEnvir,SYSargsList-method |
Man page
|
| wf |
Man page
|
| wf,SYSargs2-method |
Man page
|
| write.clt |
Source code
|
| write.yml |
Source code
|
| writeParamFiles |
Man page
Source code
|
| writeSE |
Source code
|
| writeTargets |
Man page
Source code
|
| writeTargetsRef |
Man page
Source code
|
| writeTargetsout |
Man page
Source code
|
| write_SYSargsList |
Man page
Source code
|
| yamlinput |
Man page
Man page
|
| yamlinput,SYSargs2-method |
Man page
|
| yamlinput,SYSargsList-method |
Man page
|
| yamlinput<- |
Man page
Man page
|
| yamlinput<-,SYSargs2,ANY,ANY-method |
Man page
|
| yamlinput<-,SYSargs2-method |
Man page
|
| yamlinput<-,SYSargsList-method |
Man page
|
