API for tgirke/systemPipeR
systemPipeR: NGS workflow and report generation environment

Global functions
$,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
.addNodeDecor Source code
.allAnnot Source code
.bashRStep Source code
.bashSysStep Source code
.buildDF Source code
.buildTree Source code
.catBase Source code
.catCmdRaw Source code
.catInputs Source code
.catOutputs Source code
.check.output.sysargs2 Source code
.checkOutArgs2 Source code
.check_write_SYSargsList Source code
.cmdToCwl Source code
.codingReport Source code
.collapseSteps Source code
.cwlAppend Source code
.cwlIndexTrim Source code
.cwlRename Source code
.cwlReplace Source code
.dirProject Source code
.findBranch Source code
.gene2GOlist Source code
.getSRAfastq Source code
.makeBam Source code
.modifyCwlParse Source code
.moduleload Source code
.outList2DF Source code
.outputTargets Source code
.parseInStr Source code
.parseNewIn Source code
.parseNewOut Source code
.parseOutStr Source code
.readGOorg Source code
.recommendBranch Source code
.renderWFsingle Source code
.resizeFeature Source code
.sal2rmd_rstep Source code
.sal2rmd_sysstep Source code
.sampleDFgene2GO Source code
.showHelper Source code
.statusPending Source code
.statusSummary Source code
.stepDuration Source code
.subsetReadsByMappingRegion Source code
.sysargsrunCommandline Source code
.tryRcode Source code
.tryRunC Source code
.updateAfterRunC 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
SEobj Man page
SEobj,SYSargsList-method Man page
SPRdata Man page 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,ANY-method Man page
[[,LineWise,ANY,missing-method Man page
[[,SYSargs2,ANY,missing-method Man page
[[,SYSargsList,ANY,ANY-method Man page
[[,SYSargsList,ANY,missing-method Man page
[[<-,EnvModules,ANY,ANY,ANY-method Man page
[[<-,EnvModules-method Man page
[[<-,LineWise,ANY,ANY,ANY-method Man page
[[<-,SYSargs2,ANY,ANY,ANY-method Man page
[[<-,SYSargsList,ANY,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
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
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
clt Man page
clt,SYSargs2-method Man page
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 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
createParamFiles Man page Source code
createWF Source code
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
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
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
populateCommandline Source code
predORF Man page Source code
preprocessReads Man page Source code
printParam Man page Source code
projectInfo Man page
projectInfo,SYSargsList-method Man page
readComp Man page Source code
read_SYSargsList Source code
reference Man page
reference,SYSargs-method Man page
reference-methods Man page
renameParam 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
renderReport 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
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,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 Source code
sal2rmd 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
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 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
tryCL Man page
tryCMD Man page
tryPath Man page
updateColumn<- Man page
updateColumn<-,SYSargsList-method Man page
updateWF Man page Source code
varSummary Man page Source code
variantReport Man page
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
writeTargetsRef Man page Source code
writeTargetsout Man page
write_SYSargsList 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
tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.