systemPipeR-package	systemPipeR-package
$,EnvModules-method	EnvModules-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
alignStats	alignStats
as.list,INTERSECTset-method	INTERSECTset-class
as.list,VENNset-method	VENNset-class
available_modules,EnvModules-method	EnvModules-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.output	check.output
clt	sysargs2-methods
clt,SYSargs2-method	SYSargs2-class
clt-methods	sysargs2-methods
clusterRun	clusterRun
cmdlist	sysargs2-methods
cmdlist,SYSargs2-method	SYSargs2-class
cmdlist-methods	sysargs2-methods
codeSteps	sysargslist-methods
codeSteps,SYSargsList-method	SYSargsList-class
codeSteps-methods	sysargslist-methods
coerce,EnvModules,list-method	EnvModules-class
coerce,list,catDB-method	catDB-class
coerce,list,EnvModules-method	EnvModules-class
coerce,list,INTERSECTset-method	INTERSECTset-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
cores	sysargs
cores,SYSargs-method	SYSargs-class
cores-methods	sysargs
countRangeset	countRangeset
createWF	createWF
cwlfiles	sysargs2-methods
cwlfiles,SYSargs2-method	SYSargs2-class
cwlfiles-methods	sysargs2-methods
dataWF	sysargslist-methods
dataWF,SYSargsList-method	SYSargsList-class
dataWF-methods	sysargslist-methods
default_modules,EnvModules-method	EnvModules-class
EnvModules,EnvModules-method	EnvModules-class
EnvModules-class	EnvModules-class
evalCode	evalCode
featureCoverage	featureCoverage
featuretypeCounts	featuretypeCounts
filterDEGs	filterDEGs
filterVars	filterVars
genFeatures	genFeatures
getQsubargs	getQsubargs
goBarplot	GOHyperGAll
GOCluster_Report	GOHyperGAll
GOHyperGAll	GOHyperGAll
GOHyperGAll_Simplify	GOHyperGAll
GOHyperGAll_Subset	GOHyperGAll
idconv	catmap
idconv,catDB-method	catDB-class
idconv-methods	catmap
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
initProject	initWF
initWF	initWF
input	sysargs2-methods
input,SYSargs2-method	SYSargs2-class
input-methods	sysargs2-methods
inputvars	sysargs2-methods
inputvars,SYSargs2-method	SYSargs2-class
inputvars-methods	sysargs2-methods
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,SYSargs-method	SYSargs-class
length,SYSargs2-method	SYSargs2-class
length,SYSargsList-method	SYSargsList-class
length,VENNset-method	VENNset-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	sysargs
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,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
outpaths	sysargs
outpaths,SYSargs-method	SYSargs-class
outpaths-methods	sysargs
output	sysargs2-methods
output,SYSargs2-method	SYSargs2-class
output-methods	sysargs2-methods
output_update	output_update
overLapper	overLapper
plotfeatureCoverage	plotfeatureCoverage
plotfeaturetypeCounts	plotfeaturetypeCounts
plotWF	plotWF
predORF	predORF
preprocessReads	preprocessReads
projectWF	sysargslist-methods
projectWF,SYSargsList-method	SYSargsList-class
projectWF-methods	sysargslist-methods
qsubRun	qsubRun
readComp	readComp
reference	sysargs
reference,SYSargs-method	SYSargs-class
reference-methods	sysargs
renderReport	renderReport
renderWF	renderWF
results	sysargs
results,SYSargs-method	SYSargs-class
results-methods	sysargs
returnRPKM	returnRPKM
runCommandline	runCommandline
runDiff	runDiff
runWF	runWF
run_DESeq2	run_DESeq2
run_edgeR	run_edgeR
SampleName	sysargs
SampleName,SYSargs-method	SYSargs-class
SampleName-methods	sysargs
scaleRanges	scaleRanges
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,SYSargs-method	SYSargs-class
show,SYSargs2-method	SYSargs2-class
show,SYSargsList-method	SYSargsList-class
show,VENNset-method	VENNset-class
software	sysargs
software,SYSargs-method	SYSargs-class
software-methods	sysargs
SPRdata	SPRdata
statusWF	sysargslist-methods
statusWF,SYSargsList-method	SYSargsList-class
statusWF-methods	sysargslist-methods
stepsWF	sysargslist-methods
stepsWF,SYSargsList-method	SYSargsList-class
stepsWF-methods	sysargslist-methods
subsetWF	subsetWF
summaryWF,SYSargsList-method	SYSargsList-class
symLink2bam	symLink2bam
sysargs	sysargs
sysargs,SYSargs-method	SYSargs-class
SYSargs-class	SYSargs-class
sysargs-methods	sysargs
sysargs2	sysargs2-methods
sysargs2,SYSargs2-method	SYSargs2-class
SYSargs2-class	SYSargs2-class
sysargs2-method	sysargs2-methods
SYSargs2_steps	sysargslist-methods
SYSargs2_steps,SYSargsList-method	SYSargsList-class
SYSargs2_steps-methods	sysargslist-methods
sysargslist	sysargslist-methods
sysargslist,SYSargsList-method	SYSargsList-class
SYSargsList-class	SYSargsList-class
sysargslist-method	sysargslist-methods
sysconfig	sysargslist-methods
sysconfig,SYSargsList-method	SYSargsList-class
sysconfig-methods	sysargslist-methods
SYSproject	initWF
systemArgs	systemArgs
targets	sysargs2-methods
targets,SYSargs2-method	SYSargs2-class
targets-methods	sysargs2-methods
targets.as.df	targets.as.df
targetsheader	sysargs
targetsheader,SYSargs-method	SYSargs-class
targetsheader,SYSargs2-method	SYSargs2-class
targetsheader-methods	sysargs
targetsin	sysargs
targetsin,SYSargs-method	SYSargs-class
targetsin-methods	sysargs
targetsout	sysargs
targetsout,SYSargs-method	SYSargs-class
targetsout-methods	sysargs
tryCL	tryCL
tryPath	tryPath
variantReport	variantReport
varSummary	variantReport
vennlist	overLapper
vennlist,VENNset-method	VENNset-class
vennlist-methods	overLapper
vennPlot	vennPlot
VENNset-class	VENNset-class
wf	sysargs2-methods
wf,SYSargs2-method	SYSargs2-class
wf-methods	sysargs2-methods
writeTargetsout	writeTargetsout
writeTargetsRef	writeTargetsRef
yamlinput	sysargs2-methods
yamlinput,SYSargs2-method	SYSargs2-class
yamlinput-methods	sysargs2-methods
[,EnvModules,ANY,ANY,ANY-method	EnvModules-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
[[,SYSargs2,ANY,missing-method	SYSargs2-class
[[,SYSargsList,ANY,missing-method	SYSargsList-class
[[<-,EnvModules,ANY,ANY,ANY-method	EnvModules-class
[[<-,EnvModules-method	EnvModules-class
[[<-,SYSargs2,ANY,ANY,ANY-method	SYSargs2-class
[[<-,SYSargsList,ANY,ANY,ANY-method	SYSargsList-class
