systemPipeR-package	systemPipeR-package
$,EnvModules-method	EnvModules-class
$,LineWise-method	LineWise-class
$,SYSargs2-method	SYSargs2-class
$,SYSargsList-method	SYSargsList-class
addAssay	add-methods
addAssay,SummarizedExperiment-method	add-methods
addAssay-methods	add-methods
addMetadata	add-methods
addMetadata,SummarizedExperiment-method	add-methods
addMetadata-methods	add-methods
addResources	SYSargsList-class
addResources,SYSargsList-method	SYSargsList-class
alignStats	alignStats
appendCodeLine,LineWise-method	LineWise-class
appendCodeLine<-	SYSargsList-class
appendCodeLine<-,LineWise-method	LineWise-class
appendCodeLine<-,SYSargsList-method	SYSargsList-class
appendParam	ParamFiles
appendParam2	ParamFiles2
appendStep<-	SYSargsList-class
appendStep<-,SYSargsList-method	SYSargsList-class
as.list,INTERSECTset-method	INTERSECTset-class
as.list,VENNset-method	VENNset-class
available_modules,EnvModules-method	EnvModules-class
baseCommand	SYSargsList-class
baseCommand,SYSargs2-method	SYSargs2-class
baseCommand,SYSargsList-method	SYSargsList-class
catDB-class	catDB-class
catlist	catmap
catlist,catDB-method	catDB-class
catlist-methods	catmap
catmap	catmap
catmap,catDB-method	catDB-class
catmap-methods	catmap
check.outfiles	check.output
check.output	check.output
clt	SYSargs2-class
clt,SYSargs2-method	SYSargs2-class
clusterRun	clusterRun
cmdlist	SYSargsList-class
cmdlist,SYSargs2-method	SYSargs2-class
cmdlist,SYSargsList-method	SYSargsList-class
cmdToCwl	SYSargs2-class
cmdToCwl,SYSargs2-method	SYSargs2-class
cmdToCwl<-	SYSargs2-class
cmdToCwl<-,SYSargs2-method	SYSargs2-class
codeChunkStart	LineWise-class
codeChunkStart,LineWise-method	LineWise-class
codeLine	SYSargsList-class
codeLine,LineWise-method	LineWise-class
codeLine,SYSargsList-method	SYSargsList-class
coerce,EnvModules,list-method	EnvModules-class
coerce,LineWise,list-method	LineWise-class
coerce,list,catDB-method	catDB-class
coerce,list,EnvModules-method	EnvModules-class
coerce,list,INTERSECTset-method	INTERSECTset-class
coerce,list,LineWise-method	LineWise-class
coerce,list,SYSargs-method	SYSargs-class
coerce,list,SYSargs2-method	SYSargs2-class
coerce,list,SYSargsList-method	SYSargsList-class
coerce,list,VENNset-method	VENNset-class
coerce,SYSargs2,list-method	SYSargs2-class
coerce,SYSargsList,list-method	SYSargsList-class
combineVarReports	variantReport
complexitylevels	overLapper
complexitylevels,INTERSECTset-method	INTERSECTset-class
complexitylevels,VENNset-method	VENNset-class
complexitylevels-methods	overLapper
config.param	config.param
configWF	configWF
copyEnvir	SYSargsList-class
copyEnvir,SYSargsList-method	SYSargsList-class
cores	sysargs
cores,SYSargs-method	SYSargs-class
cores-methods	sysargs
countRangeset	countRangeset
createParam	createParamFiles
createParamFiles	createParamFiles
cwlFilesUpdate	cwlFilesUpdate
default_modules,EnvModules-method	EnvModules-class
dependency	SYSargsList-class
dependency,LineWise-method	LineWise-class
dependency,SYSargsList-method	SYSargsList-class
dependency<-	SYSargsList-class
dependency<-,SYSargsList-method	SYSargsList-class
EnvModules,EnvModules-method	EnvModules-class
EnvModules-class	EnvModules-class
evalCode	evalCode
featureCoverage	featureCoverage
featuretypeCounts	featuretypeCounts
files	SYSargs2-class
files,LineWise-method	LineWise-class
files,SYSargs2-method	SYSargs2-class
filterDEGs	filterDEGs
filterVars	filterVars
genFeatures	genFeatures
getColumn	SYSargsList-class
getColumn,SYSargsList-method	SYSargsList-class
goBarplot	GOHyperGAll
GOCluster_Report	GOHyperGAll
GOHyperGAll	GOHyperGAll
GOHyperGAll_Simplify	GOHyperGAll
GOHyperGAll_Subset	GOHyperGAll
idconv	catmap
idconv,catDB-method	catDB-class
idconv-methods	catmap
importWF	importWF
infile1	sysargs
infile1,SYSargs-method	SYSargs-class
infile1,SYSargs2-method	SYSargs2-class
infile1-methods	sysargs
infile2	sysargs
infile2,SYSargs-method	SYSargs-class
infile2,SYSargs2-method	SYSargs2-class
infile2-methods	sysargs
input	SYSargs2-class
input,SYSargs2-method	SYSargs2-class
inputvars	SYSargs2-class
inputvars,SYSargs2-method	SYSargs2-class
internal_outfiles	SYSargs2-class
internal_outfiles,SYSargs2-method	SYSargs2-class
intersectlist	overLapper
intersectlist,INTERSECTset-method	INTERSECTset-class
intersectlist-methods	overLapper
intersectmatrix	overLapper
intersectmatrix,INTERSECTset-method	INTERSECTset-class
intersectmatrix,VENNset-method	VENNset-class
intersectmatrix-methods	overLapper
INTERSECTset-class	INTERSECTset-class
length,INTERSECTset-method	INTERSECTset-class
length,LineWise-method	LineWise-class
length,SYSargs-method	SYSargs-class
length,SYSargs2-method	SYSargs2-class
length,SYSargsList-method	SYSargsList-class
length,VENNset-method	VENNset-class
LineWise	LineWise-class
linewise	LineWise-class
linewise,LineWise-method	LineWise-class
LineWise-class	LineWise-class
loaded_modules,EnvModules-method	EnvModules-class
loadWF	loadWorkflow
loadWorkflow	loadWorkflow
makeCATdb	GOHyperGAll
mergeBamByFactor	mergeBamByFactor
module	moduleload
moduleAvail	moduleload
moduleClear	moduleload
modulecmd,EnvModules-method	EnvModules-class
moduleInit	moduleload
modulelist	moduleload
moduleload	moduleload
modules	SYSargs2-class
modules,SYSargs-method	SYSargs-class
modules,SYSargs2-method	SYSargs2-class
modules-methods	sysargs
moduleUnload	moduleload
names,catDB-method	catDB-class
names,EnvModules-method	EnvModules-class
names,INTERSECTset-method	INTERSECTset-class
names,LineWise-method	LineWise-class
names,SYSargs-method	SYSargs-class
names,SYSargs2-method	SYSargs2-class
names,SYSargsList-method	SYSargsList-class
names,VENNset-method	VENNset-class
olBarplot	olBarplot
olRanges	olRanges
other	sysargs
other,SYSargs-method	SYSargs-class
other-methods	sysargs
outfile1	sysargs
outfile1,SYSargs-method	SYSargs-class
outfile1-methods	sysargs
outfiles	SYSargsList-class
outfiles,SYSargsList-method	SYSargsList-class
outpaths	sysargs
outpaths,SYSargs-method	SYSargs-class
outpaths-methods	sysargs
output	SYSargs2-class
output,SYSargs2-method	SYSargs2-class
output_update	output_update
overLapper	overLapper
plotfeatureCoverage	plotfeatureCoverage
plotfeaturetypeCounts	plotfeaturetypeCounts
plotWF	plotWF
plotwfOutput	plotWF
predORF	predORF
preprocessReads	preprocessReads
printParam	ParamFiles
printParam2	ParamFiles2
projectInfo	SYSargsList-class
projectInfo,SYSargsList-method	SYSargsList-class
readComp	readComp
reference	sysargs
reference,SYSargs-method	SYSargs-class
reference-methods	sysargs
removeParam2	ParamFiles2
renameParam	ParamFiles
renameParam2	ParamFiles2
renameStep<-	SYSargsList-class
renameStep<-,SYSargsList-method	SYSargsList-class
renderLogs	renderLogs
renderPlotwf	plotWF
renderReport	renderReport
renderWF	loadWorkflow
replaceCodeLine,LineWise-method	LineWise-class
replaceCodeLine<-	SYSargsList-class
replaceCodeLine<-,LineWise-method	LineWise-class
replaceCodeLine<-,SYSargsList-method	SYSargsList-class
replaceParam	ParamFiles
replaceParam2	ParamFiles2
replaceStep<-	SYSargsList-class
replaceStep<-,SYSargsList-method	SYSargsList-class
results	sysargs
results,SYSargs-method	SYSargs-class
results-methods	sysargs
returnRPKM	returnRPKM
rmdPath	LineWise-class
rmdPath,LineWise-method	LineWise-class
runCommandline	runCommandline
runDiff	runDiff
runInfo	SYSargsList-class
runInfo,LineWise-method	LineWise-class
runInfo,SYSargsList-method	SYSargsList-class
runWF	runWF
run_DESeq2	run_DESeq2
run_edgeR	run_edgeR
sal2bash	sal2bash
sal2rmd	sal2rmd
SampleName	SYSargsList-class
SampleName,SYSargs-method	SYSargs-class
SampleName,SYSargs2-method	SYSargs2-class
SampleName,SYSargsList-method	SYSargsList-class
SampleName-methods	sysargs
scaleRanges	scaleRanges
SE	SYSargsList-class
SE,SYSargsList-method	SYSargsList-class
seeFastq	seeFastq
seeFastqPlot	seeFastq
setlist	overLapper
setlist,INTERSECTset-method	INTERSECTset-class
setlist,VENNset-method	VENNset-class
setlist-methods	overLapper
show,catDB-method	catDB-class
show,EnvModules-method	EnvModules-class
show,INTERSECTset-method	INTERSECTset-class
show,LineWise-method	LineWise-class
show,SYSargs-method	SYSargs-class
show,SYSargs2-method	SYSargs2-class
show,SYSargsList-method	SYSargsList-class
show,VENNset-method	VENNset-class
showDF	showDF
software	sysargs
software,SYSargs-method	SYSargs-class
software-methods	sysargs
SPRproject	SPRproject
status	SYSargs2-class
status,LineWise-method	LineWise-class
status,SYSargs2-method	SYSargs2-class
statusWF	SYSargsList-class
statusWF,SYSargsList-method	SYSargsList-class
stepName	SYSargsList-class
stepName,LineWise-method	LineWise-class
stepName,SYSargsList-method	SYSargsList-class
stepsWF	SYSargsList-class
stepsWF,SYSargsList-method	SYSargsList-class
subset	SYSargsList-class
subset,SYSargsList-method	SYSargsList-class
subsetParam	ParamFiles
subsetWF	subsetWF
symLink2bam	symLink2bam
sysargs	sysargs
sysargs,SYSargs-method	SYSargs-class
SYSargs-class	SYSargs-class
sysargs-methods	sysargs
sysargs2	SYSargs2-class
sysargs2,SYSargs2-method	SYSargs2-class
SYSargs2-class	SYSargs2-class
SYSargsList	SYSargsList
sysargslist	SYSargsList-class
sysargslist,SYSargsList-method	SYSargsList-class
SYSargsList-class	SYSargsList-class
systemArgs	systemArgs
targets	SYSargs2-class
targets,SYSargs2-method	SYSargs2-class
targets.as.df	targets.as.df
targets.as.list	targets.as.df
targetsheader	SYSargsList-class
targetsheader,SYSargs-method	SYSargs-class
targetsheader,SYSargs2-method	SYSargs2-class
targetsheader,SYSargsList-method	SYSargsList-class
targetsheader-methods	sysargs
targetsin	sysargs
targetsin,SYSargs-method	SYSargs-class
targetsin-methods	sysargs
targetsout	sysargs
targetsout,SYSargs-method	SYSargs-class
targetsout-methods	sysargs
targetsWF	SYSargsList-class
targetsWF,SYSargsList-method	SYSargsList-class
targets_connection	SYSargsList-class
targets_connection,SYSargsList-method	SYSargsList-class
trimbatch	trimbatch
tryCL	tryCMD
tryCMD	tryCMD
tryPath	tryPath
updateColumn<-	SYSargsList-class
updateColumn<-,SYSargsList-method	SYSargsList-class
updateWF	loadWorkflow
variantReport	variantReport
varSummary	variantReport
vennlist	overLapper
vennlist,VENNset-method	VENNset-class
vennlist-methods	overLapper
vennPlot	vennPlot
VENNset-class	VENNset-class
viewEnvir	SYSargsList-class
viewEnvir,SYSargsList-method	SYSargsList-class
wf	SYSargs2-class
wf,SYSargs2-method	SYSargs2-class
writeParamFiles	createParamFiles
writeTargets	writeTargets
writeTargetsout	writeTargetsout
writeTargetsRef	writeTargetsRef
write_SYSargsList	write_SYSargsList
yamlinput	SYSargsList-class
yamlinput,SYSargs2-method	SYSargs2-class
yamlinput,SYSargsList-method	SYSargsList-class
yamlinput<-	SYSargsList-class
yamlinput<-,SYSargs2,ANY,ANY-method	SYSargs2-class
yamlinput<-,SYSargs2-method	SYSargs2-class
yamlinput<-,SYSargsList-method	SYSargsList-class
[,EnvModules,ANY,ANY,ANY-method	EnvModules-class
[,LineWise,ANY,ANY,ANY-method	LineWise-class
[,SYSargs,ANY,ANY,ANY-method	SYSargs-class
[,SYSargs2,ANY,ANY,ANY-method	SYSargs2-class
[,SYSargsList,ANY,ANY,ANY-method	SYSargsList-class
[[,EnvModules,ANY,ANY-method	EnvModules-class
[[,EnvModules,ANY,missing-method	EnvModules-class
[[,LineWise,ANY,missing-method	LineWise-class
[[,SYSargs2,ANY,missing-method	SYSargs2-class
[[,SYSargsList,ANY,missing-method	SYSargsList-class
[[<-,EnvModules,ANY,ANY,ANY-method	EnvModules-class
[[<-,EnvModules,ANY,ANY-method	EnvModules-class
[[<-,EnvModules-method	EnvModules-class
[[<-,LineWise,ANY,ANY,ANY-method	LineWise-class
[[<-,LineWise,ANY,ANY-method	LineWise-class
[[<-,SYSargs2,ANY,ANY,ANY-method	SYSargs2-class
[[<-,SYSargs2,ANY,ANY-method	SYSargs2-class
[[<-,SYSargsList,ANY,ANY,ANY-method	SYSargsList-class
[[<-,SYSargsList,ANY,ANY-method	SYSargsList-class
