$,SYSargs2-method	SYSargs2-class
$,SYSargs2Pipe-method	SYSargs2Pipe-class
alignStats	alignStats
as.list,INTERSECTset-method	INTERSECTset-class
as.list,VENNset-method	VENNset-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
clt	SYSargs2list-methods
clt,SYSargs2-method	SYSargs2-class
clt-methods	SYSargs2list-methods
clusterRun	clusterRun
cmdlist	SYSargs2list-methods
cmdlist,SYSargs2-method	SYSargs2-class
cmdlist-methods	SYSargs2list-methods
coerce,list,catDB-method	catDB-class
coerce,list,INTERSECTset-method	INTERSECTset-class
coerce,list,SYSargs-method	SYSargs-class
coerce,list,SYSargs2-method	SYSargs2-class
coerce,list,SYSargs2Pipe-method	SYSargs2Pipe-class
coerce,list,VENNset-method	VENNset-class
coerce,SYSargs2,list-method	SYSargs2-class
coerce,SYSargs2Pipe,list-method	SYSargs2Pipe-class
combineVarReports	variantReport
complexitylevels	overLapper
complexitylevels,INTERSECTset-method	INTERSECTset-class
complexitylevels,VENNset-method	VENNset-class
complexitylevels-methods	overLapper
cores	sysargs
cores,SYSargs-method	SYSargs-class
cores-methods	sysargs
countRangeset	countRangeset
cwlfiles	SYSargs2list-methods
cwlfiles,SYSargs2-method	SYSargs2-class
cwlfiles-methods	SYSargs2list-methods
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
input	SYSargs2list-methods
input,SYSargs2-method	SYSargs2-class
input-methods	SYSargs2list-methods
inputvars	SYSargs2list-methods
inputvars,SYSargs2-method	SYSargs2-class
inputvars-methods	SYSargs2list-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,SYSargs2Pipe-method	SYSargs2Pipe-class
length,VENNset-method	VENNset-class
loadWorkflow	loadWorkflow
makeCATdb	GOHyperGAll
mergeBamByFactor	mergeBamByFactor
module	module
modulelist	moduleload
moduleload	moduleload
modules	sysargs
modules,SYSargs-method	SYSargs-class
modules,SYSargs2-method	SYSargs2-class
modules-methods	sysargs
names,catDB-method	catDB-class
names,INTERSECTset-method	INTERSECTset-class
names,SYSargs-method	SYSargs-class
names,SYSargs2-method	SYSargs2-class
names,SYSargs2Pipe-method	SYSargs2Pipe-class
names,VENNset-method	VENNset-class
olBarplot	olBarplot
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	SYSargs2list-methods
output,SYSargs2-method	SYSargs2-class
output-methods	SYSargs2list-methods
output_update	output_update
overLapper	overLapper
plotfeatureCoverage	plotfeatureCoverage
plotfeaturetypeCounts	plotfeaturetypeCounts
predORF	predORF
preprocessReads	preprocessReads
qsubRun	qsubRun
readComp	readComp
reference	sysargs
reference,SYSargs-method	SYSargs-class
reference-methods	sysargs
renderWF	renderWF
results	sysargs
results,SYSargs-method	SYSargs-class
results-methods	sysargs
returnRPKM	returnRPKM
runCommandline	runCommandline
runDiff	runDiff
run_DESeq2	run_DESeq2
run_edgeR	run_edgeR
run_track	run_track
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,INTERSECTset-method	INTERSECTset-class
show,SYSargs-method	SYSargs-class
show,SYSargs2-method	SYSargs2-class
show,SYSargs2Pipe-method	SYSargs2Pipe-class
show,VENNset-method	VENNset-class
software	sysargs
software,SYSargs-method	SYSargs-class
software-methods	sysargs
subsetWF	subsetWF
summaryWF	SYSargs2Pipe-methods
summaryWF,SYSargs2Pipe-method	SYSargs2Pipe-class
summaryWF-methods	SYSargs2Pipe-methods
symLink2bam	symLink2bam
sysargs	sysargs
sysargs,SYSargs-method	SYSargs-class
SYSargs-class	SYSargs-class
sysargs-methods	sysargs
SYSargs2-class	SYSargs2-class
SYSargs2list	SYSargs2list-methods
SYSargs2list,SYSargs2-method	SYSargs2-class
SYSargs2list-method	SYSargs2list-methods
SYSargs2Pipe-class	SYSargs2Pipe-class
SYSargs2Pipe-method	SYSargs2Pipe-methods
SYSargs2Pipe_ls	SYSargs2Pipe-methods
SYSargs2Pipe_ls,SYSargs2Pipe-method	SYSargs2Pipe-class
systemArgs	systemArgs
targets	SYSargs2list-methods
targets,SYSargs2-method	SYSargs2-class
targets-methods	SYSargs2list-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
track	SYSargs2Pipe-methods
track,SYSargs2Pipe-method	SYSargs2Pipe-class
track-methods	SYSargs2Pipe-methods
variantReport	variantReport
varSummary	variantReport
vennlist	overLapper
vennlist,VENNset-method	VENNset-class
vennlist-methods	overLapper
vennPlot	vennPlot
VENNset-class	VENNset-class
wf	SYSargs2list-methods
wf,SYSargs2-method	SYSargs2-class
wf-methods	SYSargs2list-methods
WF_steps	SYSargs2Pipe-methods
WF_steps,SYSargs2Pipe-method	SYSargs2Pipe-class
WF_steps-methods	SYSargs2Pipe-methods
writeTargetsout	writeTargetsout
writeTargetsRef	writeTargetsRef
yamlinput	SYSargs2list-methods
yamlinput,SYSargs2-method	SYSargs2-class
yamlinput-methods	SYSargs2list-methods
[,SYSargs,ANY,ANY,ANY-method	SYSargs-class
[,SYSargs2,ANY,ANY,ANY-method	SYSargs2-class
[,SYSargs2Pipe,ANY,ANY,ANY-method	SYSargs2Pipe-class
[[,SYSargs2,ANY,missing-method	SYSargs2-class
[[,SYSargs2Pipe,ANY,ANY-method	SYSargs2Pipe-class
[[<-,SYSargs2,ANY,ANY,ANY-method	SYSargs2-class
[[<-,SYSargs2Pipe,ANY,ANY,ANY-method	SYSargs2Pipe-class
