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
clusterRun	clusterRun
coerce,list,catDB-method	catDB-class
coerce,list,INTERSECTset-method	INTERSECTset-class
coerce,list,SYSargs-method	SYSargs-class
coerce,list,VENNset-method	VENNset-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
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-methods	sysargs
infile2	sysargs
infile2,SYSargs-method	SYSargs-class
infile2-methods	sysargs
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,VENNset-method	VENNset-class
makeCATdb	GOHyperGAll
mergeBamByFactor	mergeBamByFactor
modulelist	moduleload
moduleload	moduleload
modules	sysargs
modules,SYSargs-method	SYSargs-class
modules-methods	sysargs
names,catDB-method	catDB-class
names,INTERSECTset-method	INTERSECTset-class
names,SYSargs-method	SYSargs-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
overLapper	overLapper
plotfeatureCoverage	plotfeatureCoverage
plotfeaturetypeCounts	plotfeaturetypeCounts
predORF	predORF
preprocessReads	preprocessReads
qsubRun	qsubRun
readComp	readComp
reference	sysargs
reference,SYSargs-method	SYSargs-class
reference-methods	sysargs
results	sysargs
results,SYSargs-method	SYSargs-class
results-methods	sysargs
returnRPKM	returnRPKM
runCommandline	runCommandline
runDiff	runDiff
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,INTERSECTset-method	INTERSECTset-class
show,SYSargs-method	SYSargs-class
show,VENNset-method	VENNset-class
software	sysargs
software,SYSargs-method	SYSargs-class
software-methods	sysargs
symLink2bam	symLink2bam
sysargs	sysargs
sysargs,SYSargs-method	SYSargs-class
SYSargs-class	SYSargs-class
sysargs-methods	sysargs
systemArgs	systemArgs
targetsheader	sysargs
targetsheader,SYSargs-method	SYSargs-class
targetsheader-methods	sysargs
targetsin	sysargs
targetsin,SYSargs-method	SYSargs-class
targetsin-methods	sysargs
targetsout	sysargs
targetsout,SYSargs-method	SYSargs-class
targetsout-methods	sysargs
variantReport	variantReport
varSummary	variantReport
vennlist	overLapper
vennlist,VENNset-method	VENNset-class
vennlist-methods	overLapper
vennPlot	vennPlot
VENNset-class	VENNset-class
writeTargetsout	writeTargetsout
writeTargetsRef	writeTargetsRef
[,SYSargs,ANY,ANY,ANY-method	SYSargs-class
