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