$,UTR3eSet-method	UTR3eSet-class
$<-,UTR3eSet-method	UTR3eSet-class
.onAttach	dot-onAttach
addChr2Exclude	addChr2Exclude
addInPASEnsDb	addInPASEnsDb
addInPASGenome	addInPASGenome
addInPASOutputDirectory	addInPASOutputDirectory
addInPASTxDb	addInPASTxDb
addLockName	addLockName
adjust_distalCPs	adjust_distalCPs
adjust_proximalCPs	adjust_proximalCPs
adjust_proximalCPsByNBC	adjust_proximalCPsByNBC
adjust_proximalCPsByPWM	adjust_proximalCPsByPWM
assemble_allCov	assemble_allCov
assign_feature	assign_feature
calculate_mse	calculate_mse
coerce,UTR3eSet,ExpressionSet-method	UTR3eSet-class
coerce,UTR3eSet,GRanges-method	UTR3eSet-class
compensation	compensation
extract_UTR3Anno	extract_UTR3Anno
fft.smooth	fft.smooth
filter_testOut	filter_testOut
find_minMSEDistr	find_minMSEDistr
find_valleyBySpline	find_valleyBySpline
gcComp	gcComp
gcContents	gcContents
getChr2Exclude	getChr2Exclude
getInPASEnsDb	getInPASEnsDb
getInPASGenome	getInPASGenome
getInPASOutputDirectory	getInPASOutputDirectory
getInPASSQLiteDb	getInPASSQLiteDb
getInPASTxDb	getInPASTxDb
getLockName	getLockName
get_chromosomes	get_chromosomes
get_depthWeight	get_depthWeight
get_lastCDSUTR3	get_lastCDSUTR3
get_PAscore	get_PAscore
get_PAscore2	get_PAscore2
get_regionCov	get_regionCov
get_seqLen	get_seqLen
get_ssRleCov	get_ssRleCov
get_totalCov	get_totalCov
get_usage4plot	get_usage4plot
get_UTR3CDS	get_UTR3CDS
get_UTR3eSet	get_UTR3eSet
get_UTR3region	get_UTR3region
get_UTR3TotalCov	get_UTR3TotalCov
get_zScoreCutoff	get_zScoreCutoff
InPAS	InPAS
mapComp	mapComp
parse_TxDb	parse_TxDb
plot_utr3Usage	plot_utr3Usage
polish_CPs	polish_CPs
remove_convergentUTR3s	remove_convergentUTR3s
run_coverageQC	run_coverageQC
run_fisherExactTest	run_fisherExactTest
run_limmaAnalysis	run_limmaAnalysis
run_singleGroupAnalysis	run_singleGroupAnalysis
run_singleSampleAnalysis	run_singleSampleAnalysis
search_CPs	search_CPs
search_distalCPs	search_distalCPs
search_proximalCPs	search_proximalCPs
setup_CPsSearch	setup_CPsSearch
setup_GSEA	setup_GSEA
setup_parCPsSearch	setup_parCPsSearch
setup_sqlitedb	setup_sqlitedb
set_globals	set_globals
show,UTR3eSet-method	UTR3eSet-class
test_dPDUI	test_dPDUI
trim_seqnames	trim_seqnames
utr3.mm10	utr3.mm10
UTR3eSet-class	UTR3eSet-class
