ORFik-package	ORFik-package
addCdsOnLeaderEnds	addCdsOnLeaderEnds
addNewTSSOnLeaders	addNewTSSOnLeaders
add_pseudo_5utrs_txdb_if_needed	add_pseudo_5utrs_txdb_if_needed
alignmentFeatureStatistics	alignmentFeatureStatistics
allFeaturesHelper	allFeaturesHelper
appendZeroes	appendZeroes
append_gene_symbols	append_gene_symbols
artificial.orfs	artificial.orfs
assignAnnotations	assignAnnotations
assignFirstExonsStartSite	assignFirstExonsStartSite
assignLastExonsStopSite	assignLastExonsStopSite
assignTSSByCage	assignTSSByCage
asTX	asTX
bamVarName	bamVarName
bamVarNamePicker	bamVarNamePicker
batchNames	batchNames
bedToGR	bedToGR
browseSRA	browseSRA
canonical_isoforms	canonical_isoforms
canonical_isoforms,experiment-method	canonical_isoforms-experiment-method
cellLineNames	cellLineNames
cellTypeNames	cellTypeNames
changePointAnalysis	changePointAnalysis
checkRFP	checkRFP
checkRNA	checkRNA
codonSumsPerGroup	codonSumsPerGroup
codon_usage	codon_usage
codon_usage_exp	codon_usage_exp
codon_usage_plot	codon_usage_plot
collapse.by.scores	collapse.by.scores
collapse.fastq	collapse.fastq
collapseDuplicatedReads	collapseDuplicatedReads
collapseDuplicatedReads,data.table-method	collapseDuplicatedReads-data.table-method
collapseDuplicatedReads,GAlignmentPairs-method	collapseDuplicatedReads-GAlignmentPairs-method
collapseDuplicatedReads,GAlignments-method	collapseDuplicatedReads-GAlignments-method
collapseDuplicatedReads,GRanges-method	collapseDuplicatedReads-GRanges-method
combn.pairs	combn.pairs
computeFeatures	computeFeatures
computeFeaturesCage	computeFeaturesCage
conditionNames	conditionNames
config	config
config.exper	config.exper
config.save	config.save
config_file	config_file
convertLibs	convertLibs
convertToOneBasedRanges	convertToOneBasedRanges
convert_bam_to_ofst	convert_bam_to_ofst
convert_to_bigWig	convert_to_bigWig
convert_to_covRle	convert_to_covRle
convert_to_covRleList	convert_to_covRleList
convert_to_fstWig	convert_to_fstWig
correlation.plots	correlation.plots
cor_plot	cor_plot
cor_table	cor_table
countOverlapsW	countOverlapsW
countTable	countTable
countTable_regions	countTable_regions
coverageByTranscriptC	coverageByTranscriptC
coverageByTranscriptFST	coverageByTranscriptFST
coverageByTranscriptW	coverageByTranscriptW
coverageGroupings	coverageGroupings
coverageHeatMap	coverageHeatMap
coveragePerTiling	coveragePerTiling
coverageScorings	coverageScorings
coverage_to_dt	coverage_to_dt
covRle	covRle
covRle-class	covRle-class
covRleFromGR	covRleFromGR
covRleList	covRleList
covRleList-class	covRleList-class
create.experiment	create.experiment
defineIsoform	defineIsoform
defineTrailer	defineTrailer
DEG.analysis	DEG.analysis
DEG.plot.static	DEG.plot.static
DEG_gorilla	DEG_gorilla
DEG_model	DEG_model
DEG_model_results	DEG_model_results
DEG_model_simple	DEG_model_simple
design,experiment-method	design-experiment-method
detectRibosomeShifts	detectRibosomeShifts
detect_ribo_orfs	detect_ribo_orfs
disengagementScore	disengagementScore
distanceToFollowing	distanceToFollowing
distanceToPreceding	distanceToPreceding
distToCds	distToCds
distToTSS	distToTSS
download.ebi	download.ebi
download.SRA	download.SRA
download.SRA.metadata	download.SRA.metadata
download_gene_homologues	download_gene_homologues
download_gene_info	download_gene_info
downstreamFromPerGroup	downstreamFromPerGroup
downstreamN	downstreamN
downstreamOfPerGroup	downstreamOfPerGroup
DTEG.analysis	DTEG.analysis
DTEG.plot	DTEG.plot
entropy	entropy
envExp	envExp
envExp,experiment-method	envExp-experiment-method
envExp<-	envExp-set
envExp<-,experiment-method	envExp-set-experiment-method
exists.ftp.dir.fast	exists.ftp.dir.fast
exists.ftp.file.fast	exists.ftp.file.fast
exonsWithPseudoIntronsPerGroup	exonsWithPseudoIntronsPerGroup
experiment	experiment-class
experiment-class	experiment-class
experiment.colors	experiment.colors
export.bed12	export.bed12
export.bedo	export.bedo
export.bedoc	export.bedoc
export.bigWig	export.bigWig
export.fstwig	export.fstwig
export.ofst	export.ofst
export.ofst,GAlignmentPairs-method	export.ofst-GAlignmentPairs-method
export.ofst,GAlignments-method	export.ofst-GAlignments-method
export.ofst,GRanges-method	export.ofst-GRanges-method
export.wiggle	export.wiggle
extendLeaders	extendLeaders
extendLeadersUntil	extendLeadersUntil
extendsTSSexons	extendsTSSexons
extendTrailers	extendTrailers
extendTrailersUntil	extendTrailersUntil
extract_run_id	extract_run_id
f	f
f,covRle-method	f-covRle-method
filepath	filepath
file_ext_without_compression	file_ext_without_compression
filterCage	filterCage
filterExtremePeakGenes	filterExtremePeakGenes
filterTranscripts	filterTranscripts
filterUORFs	filterUORFs
fimport	fimport
findFa	findFa
findFromPath	findFromPath
findLibrariesInFolder	findLibrariesInFolder
findMapORFs	findMapORFs
findMaxPeaks	findMaxPeaks
findNewTSS	findNewTSS
findNGSPairs	findNGSPairs
findORFs	findORFs
findORFsFasta	findORFsFasta
findPeaksPerGene	findPeaksPerGene
findUORFs	findUORFs
findUORFs_exp	findUORFs_exp
find_url_ebi	find_url_ebi
find_url_ebi_safe	find_url_ebi_safe
firstEndPerGroup	firstEndPerGroup
firstExonPerGroup	firstExonPerGroup
firstStartPerGroup	firstStartPerGroup
fix_malformed_gff	fix_malformed_gff
flankPerGroup	flankPerGroup
floss	floss
footprints.analysis	footprints.analysis
fpkm	fpkm
fpkm_calc	fpkm_calc
fractionLength	fractionLength
fractionNames	fractionNames
fread.bed	fread.bed
gcContent	gcContent
geneToSymbol	geneToSymbol
getGAlignments	getGAlignments
getGAlignmentsPairs	getGAlignmentsPairs
getGenomeAndAnnotation	getGenomeAndAnnotation
getGRanges	getGRanges
getGtfPathFromTxdb	getGtfPathFromTxdb
getNGenesCoverage	getNGenesCoverage
getWeights	getWeights
get_bioproject_candidates	get_bioproject_candidates
get_genome_fasta	get_genome_fasta
get_genome_gtf	get_genome_gtf
get_noncoding_rna	get_noncoding_rna
get_phix_genome	get_phix_genome
get_silva_rRNA	get_silva_rRNA
get_system_usage	get_system_usage
go_analaysis_gorilla	go_analaysis_gorilla
groupGRangesBy	groupGRangesBy
groupings	groupings
gSort	gSort
hasHits	hasHits
heatMapL	heatMapL
heatMapRegion	heatMapRegion
heatMap_single	heatMap_single
import.bedo	import.bedo
import.bedoc	import.bedoc
import.fstwig	import.fstwig
import.ofst	import.ofst
importGtfFromTxdb	importGtfFromTxdb
inhibitorNames	inhibitorNames
initiationScore	initiationScore
insideOutsideORF	insideOutsideORF
install.fastp	install.fastp
install.sratoolkit	install.sratoolkit
is.grl	is.grl
is.gr_or_grl	is.gr_or_grl
is.ORF	is.ORF
is.range	is.range
isInFrame	isInFrame
isOverlapping	isOverlapping
isPeriodic	isPeriodic
kozakHeatmap	kozakHeatmap
kozakSequenceScore	kozakSequenceScore
kozak_IR_ranking	kozak_IR_ranking
lastExonEndPerGroup	lastExonEndPerGroup
lastExonPerGroup	lastExonPerGroup
lastExonStartPerGroup	lastExonStartPerGroup
length,covRle-method	length-covRle-method
length,covRleList-method	length-covRleList-method
lengths,covRle-method	lengths-covRle-method
lengths,covRleList-method	lengths-covRleList-method
libFolder	libFolder
libFolder,experiment-method	libFolder-experiment-method
libNames	libNames
libraryTypes	libraryTypes
list.experiments	list.experiments
list.genomes	list.genomes
loadRegion	loadRegion
loadRegions	loadRegions
loadTranscriptType	loadTranscriptType
loadTxdb	loadTxdb
longestORFs	longestORFs
mainNames	mainNames
makeExonRanks	makeExonRanks
makeORFNames	makeORFNames
makeSummarizedExperimentFromBam	makeSummarizedExperimentFromBam
makeSymbols	makeSymbols
makeTxdbFromGenome	makeTxdbFromGenome
mapToGRanges	mapToGRanges
matchColors	matchColors
matchNaming	matchNaming
matchSeqStyle	matchSeqStyle
mergeFastq	mergeFastq
mergeLibs	mergeLibs
metadata.autnaming	metadata.autnaming
metaWindow	metaWindow
model.matrix,experiment-method	model.matrix-experiment-method
name	name
name,experiment-method	name-experiment-method
nrow,experiment-method	nrow-experiment-method
numCodons	numCodons
numExonsPerGroup	numExonsPerGroup
ofst_merge	ofst_merge
optimizedTranscriptLengths	optimizedTranscriptLengths
optimized_txdb_path	optimized_txdb_path
optimizeReads	optimizeReads
optimizeTranscriptRegions	optimizeTranscriptRegions
orfFrameDistributions	orfFrameDistributions
orfID	orfID
ORFik	ORFik-package
ORFik.template.experiment	ORFik.template.experiment
ORFik.template.experiment.zf	ORFik.template.experiment.zf
ORFikQC	ORFikQC
orfScore	orfScore
organism,experiment-method	organism-experiment-method
outputLibs	outputLibs
pasteDir	pasteDir
pcaExperiment	pcaExperiment
pcaPlot	pcaPlot
percentage_to_ratio	percentage_to_ratio
plotHelper	plotHelper
pmapFromTranscriptF	pmapFromTranscriptF
pmapToTranscriptF	pmapToTranscriptF
prettyScoring	prettyScoring
pseudo.transform	pseudo.transform
pseudoIntronsPerGroup	pseudoIntronsPerGroup
pSitePlot	pSitePlot
QCfolder	QCfolder
QCfolder,experiment-method	QCfolder-experiment-method
QCplots	QCplots
QCreport	QCreport
QCstats	QCstats
QCstats.plot	QCstats.plot
QC_count_tables	QC_count_tables
r	r
r,covRle-method	r-covRle-method
rankOrder	rankOrder
read.experiment	read.experiment
readBam	readBam
readBigWig	readBigWig
readLengthTable	readLengthTable
readWidths	readWidths
readWig	readWig
read_RDSQS	read_RDSQS
reassignTSSbyCage	reassignTSSbyCage
reassignTxDbByCage	reassignTxDbByCage
reduceKeepAttr	reduceKeepAttr
refFolder	refFolder
refFolder,experiment-method	refFolder-experiment-method
regionPerReadLength	regionPerReadLength
remakeTxdbExonIds	remakeTxdbExonIds
remove.experiments	remove.experiments
remove.file_ext	remove.file_ext
removeMetaCols	removeMetaCols
removeORFsWithinCDS	removeORFsWithinCDS
removeORFsWithSameStartAsCDS	removeORFsWithSameStartAsCDS
removeORFsWithSameStopAsCDS	removeORFsWithSameStopAsCDS
removeORFsWithStartInsideCDS	removeORFsWithStartInsideCDS
removeTxdbExons	removeTxdbExons
removeTxdbTranscripts	removeTxdbTranscripts
rename.SRA.files	rename.SRA.files
repNames	repNames
resFolder	resFolder
resFolder,experiment-method	resFolder-experiment-method
restrictTSSByUpstreamLeader	restrictTSSByUpstreamLeader
revElementsF	revElementsF
reverseMinusStrandPerGroup	reverseMinusStrandPerGroup
riboORFs	riboORFs
riboORFsFolder	riboORFsFolder
RiboQC.plot	RiboQC.plot
ribosomeReleaseScore	ribosomeReleaseScore
ribosomeStallingScore	ribosomeStallingScore
ribo_fft	ribo_fft
ribo_fft_plot	ribo_fft_plot
rnaNormalize	rnaNormalize
runIDs	runIDs
runIDs,experiment-method	runIDs-experiment-method
save.experiment	save.experiment
savePlot	savePlot
save_RDSQS	save_RDSQS
scaledWindowPositions	scaledWindowPositions
scoreSummarizedExperiment	scoreSummarizedExperiment
seqinfo,covRle-method	seqinfo-covRle-method
seqinfo,covRleList-method	seqinfo-covRleList-method
seqinfo,experiment-method	seqinfo-experiment-method
seqlevels,covRle-method	seqlevels-covRle-method
seqlevels,covRleList-method	seqlevels-covRleList-method
seqlevels,experiment-method	seqlevels-experiment-method
seqnames,experiment-method	seqnames-experiment-method
seqnamesPerGroup	seqnamesPerGroup
shiftFootprints	shiftFootprints
shiftFootprintsByExperiment	shiftFootprintsByExperiment
shiftPlots	shiftPlots
shifts_load	shifts_load
shifts_save	shifts_save
show,covRle-method	show-covRle-method
show,covRleList-method	show-covRleList-method
show,experiment-method	show-experiment-method
simpleLibs	simpleLibs
sortPerGroup	sortPerGroup
splitIn3Tx	splitIn3Tx
stageNames	stageNames
STAR.align.folder	STAR.align.folder
STAR.align.single	STAR.align.single
STAR.allsteps.multiQC	STAR.allsteps.multiQC
STAR.index	STAR.index
STAR.install	STAR.install
STAR.multiQC	STAR.multiQC
STAR.remove.crashed.genome	STAR.remove.crashed.genome
startCodons	startCodons
startDefinition	startDefinition
startRegion	startRegion
startRegionCoverage	startRegionCoverage
startRegionString	startRegionString
startSites	startSites
stopCodons	stopCodons
stopDefinition	stopDefinition
stopRegion	stopRegion
stopSites	stopSites
strandBool	strandBool
strandMode,covRle-method	strandMode-covRle-method
strandMode,covRleList-method	strandMode-covRleList-method
strandPerGroup	strandPerGroup
subsetCoverage	subsetCoverage
subsetToFrame	subsetToFrame
sum,covRle-method	sum-covRle-method
symbols	symbols
symbols,experiment-method	symbols-experiment-method
te.plot	te.plot
te.table	te.table
te_rna.plot	te_rna.plot
tile1	tile1
tissueNames	tissueNames
TOP.Motif.ecdf	TOP.Motif.ecdf
topMotif	topMotif
transcriptWindow	transcriptWindow
transcriptWindow1	transcriptWindow1
transcriptWindowPer	transcriptWindowPer
translationalEff	translationalEff
trimming.table	trimming.table
trim_detection	trim_detection
txNames	txNames
txNamesToGeneNames	txNamesToGeneNames
txSeqsFromFa	txSeqsFromFa
uniqueGroups	uniqueGroups
uniqueOrder	uniqueOrder
unlistGrl	unlistGrl
unlistToExtremities	unlistToExtremities
uORFSearchSpace	uORFSearchSpace
updateTxdbRanks	updateTxdbRanks
updateTxdbStartSites	updateTxdbStartSites
upstreamFromPerGroup	upstreamFromPerGroup
upstreamOfPerGroup	upstreamOfPerGroup
validateExperiments	validateExperiments
validGRL	validGRL
validSeqlevels	validSeqlevels
widthPerGroup	widthPerGroup
windowCoveragePlot	windowCoveragePlot
windowPerGroup	windowPerGroup
windowPerReadLength	windowPerReadLength
windowPerTranscript	windowPerTranscript
xAxisScaler	xAxisScaler
yAxisScaler	yAxisScaler
