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 |
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"' |
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 |
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 |
renameParam | Accessories function to modify the Command-line |
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 |
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"' |
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 |
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"' |
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"' |