basejump-package	basejump-package
%$%	reexports
%<>%	reexports
%>%	reexports
%T>%	reexports
aggregate	aggregate
aggregateCellsToSamples	aggregateCellsToSamples
aggregateCellsToSamples,SingleCellExperiment-method	aggregateCellsToSamples
aggregateCols,matrix-method	aggregate
aggregateCols,SingleCellExperiment-method	aggregate
aggregateCols,sparseMatrix-method	aggregate
aggregateCols,SummarizedExperiment-method	aggregate
aggregateFeatures	deprecated
aggregateFeatures,ANY-method	deprecated
aggregateReplicates	deprecated
aggregateReplicates,ANY-method	deprecated
aggregateRows,matrix-method	aggregate
aggregateRows,sparseMatrix-method	aggregate
aggregateRows,SummarizedExperiment-method	aggregate
aggregateSamples	deprecated
aggregateSamples,ANY-method	deprecated
annotable	makeGRanges
as.data.frame	reexports
as.data.table	reexports
as.DataFrame	reexports
as.SummarizedExperiment	reexports
assert	reexports
assertAreGeneAnnotations	deprecated
assertFormalGene2symbol	deprecated
assertFormalInterestingGroups	deprecated
assertIsAHeaderLevel	deprecated
assertIsAnImplicitInteger	deprecated
assertIsAnImplicitIntegerOrNULL	deprecated
assertIsAStringOrNULL	deprecated
assertIsColorScaleDiscreteOrNULL	deprecated
assertIsFillScaleDiscreteOrNULL	deprecated
assertIsGene2symbol	deprecated
assertIsHexColorFunctionOrNULL	deprecated
assertIsImplicitInteger	deprecated
assertIsTx2gene	deprecated
assignAndSaveData	reexports
as_tibble	reexports
atomize	reexports
autopadZeros	autopadZeros
autopadZeros,character-method	autopadZeros
autopadZeros,matrix-method	autopadZeros
autopadZeros,SummarizedExperiment-method	autopadZeros
bapply	reexports
barcodePattern	barcodePattern
basejump	basejump-package
basejumpCacheURL	basejumpCacheURL
basejump_geom_abline	ggplot2-geoms
basejump_geom_label	ggplot2-geoms
basejump_geom_label_average	ggplot2-geoms
basejump_geom_label_repel	ggplot2-geoms
basenameSansExt	reexports
broadClass	defunct
bunzip2	reexports
bzip2	reexports
camel	reexports
capitalize	reexports
cell2sample	cell2sample
cell2sample,SingleCellExperiment-method	cell2sample
checkClasses	deprecated
coerceS4ToList	reexports
collapseToString	collapseToString
collapseToString,atomic-method	collapseToString
collapseToString,data.frame-method	collapseToString
collapseToString,DataFrame-method	collapseToString
collapseToString,matrix-method	collapseToString
combine	combine
combine,SingleCellExperiment,SingleCellExperiment-method	combine
combine,SummarizedExperiment,SummarizedExperiment-method	combine
compressFile	reexports
convertGenesToSymbols	convertGenesToSymbols
convertGenesToSymbols,character-method	convertGenesToSymbols
convertGenesToSymbols,matrix-method	convertGenesToSymbols
convertGenesToSymbols,sparseMatrix-method	convertGenesToSymbols
convertGenesToSymbols,SummarizedExperiment-method	convertGenesToSymbols
convertSampleIDsToNames	convertSampleIDsToNames
convertSampleIDsToNames,SingleCellExperiment-method	convertSampleIDsToNames
convertSampleIDsToNames,SummarizedExperiment-method	convertSampleIDsToNames
convertSymbolsToGenes,SummarizedExperiment-method	convertGenesToSymbols
convertTranscriptsToGenes	convertTranscriptsToGenes
convertTranscriptsToGenes,character-method	convertTranscriptsToGenes
convertTranscriptsToGenes,matrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,sparseMatrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,SummarizedExperiment-method	convertTranscriptsToGenes
convertUCSCBuildToEnsembl	convertUCSCBuildToEnsembl
counts	counts
counts,SummarizedExperiment-method	counts
counts<-	counts
counts<-,SummarizedExperiment-method	counts
decode	reexports
decompressFile	reexports
defunct	defunct
deprecated	deprecated
detectHPC	detectHPC
detectLanes	detectLanes
detectOrganism	detectOrganism
df	df
dots	reexports
dotted	reexports
dynamicPlotlist	defunct
EggNOG	EggNOG-class
eggnog	deprecated
EggNOG-class	EggNOG-class
emptyRanges	emptyRanges
encode	reexports
ensembl	defunct
Ensembl2Entrez	Ensembl2Entrez-class
ensembl2entrez	deprecated
Ensembl2Entrez,DataFrame-method	Ensembl2Entrez-class
Ensembl2Entrez,GRanges-method	Ensembl2Entrez-class
Ensembl2Entrez,SummarizedExperiment-method	Ensembl2Entrez-class
Ensembl2Entrez-class	Ensembl2Entrez-class
export	reexports
extPattern	reexports
extractLocal	reexports
factorize	reexports
fileExt	reexports
fixNA	deprecated
flatFiles	reexports
foldChangeToLogRatio,numeric-method	logRatio
formalsList	formalsList
gender_markers	gender_markers
Gene2Symbol	Gene2Symbol-class
gene2symbol	deprecated
Gene2Symbol,DataFrame-method	Gene2Symbol-class
Gene2Symbol,GRanges-method	Gene2Symbol-class
Gene2Symbol,SummarizedExperiment-method	Gene2Symbol-class
Gene2Symbol-class	Gene2Symbol-class
gene2symbolFromGFF	defunct
gene2symbolFromGTF	defunct
geneNames	geneNames
geneNames,GRanges-method	geneNames
geneNames,SummarizedExperiment-method	geneNames
geneSynonyms	geneSynonyms
genomeMetadataNames	genomeMetadataNames
geomean	defunct
geometricMean	geometricMean
geometricMean,matrix-method	geometricMean
geometricMean,numeric-method	geometricMean
geometricMean,sparseMatrix-method	geometricMean
ggplot2-geoms	ggplot2-geoms
ggplot2-themes	ggplot2-themes
grepString	deprecated
gunzip	reexports
gzip	reexports
hasLocal	reexports
hasRownames	reexports
headtail	headtail
headtail,atomic-method	headtail
headtail,data.frame-method	headtail
headtail,DataFrame-method	headtail
headtail,GRanges-method	headtail
headtail,matrix-method	headtail
headtail,sparseMatrix-method	headtail
headtail,SummarizedExperiment-method	headtail
HGNC2Ensembl	HGNC2Ensembl-class
hgnc2ensembl	deprecated
HGNC2Ensembl-class	HGNC2Ensembl-class
hgnc2gene	deprecated
humanize	humanize
humanize,SummarizedExperiment-method	humanize
import	reexports
initDir	reexports
initializeDirectory	deprecated
interestingGroups	interestingGroups
interestingGroups,SummarizedExperiment-method	interestingGroups
interestingGroups<-,SummarizedExperiment,character-method	interestingGroups
interestingGroups<-,SummarizedExperiment,NULL-method	interestingGroups
kables	deprecated
kebab	reexports
lanePattern	lanePattern
loadData	reexports
loadDataAsName	reexports
loadRemoteData	reexports
localOrRemoteFile	reexports
logRatio	logRatio
logRatioToFoldChange,numeric-method	logRatio
makeDimnames	reexports
makeGene2Symbol	makeGene2Symbol
makeGene2SymbolFromEnsDb	makeGene2Symbol
makeGene2SymbolFromEnsembl	makeGene2Symbol
makeGene2symbolFromEnsembl	deprecated
makeGene2SymbolFromGFF	makeGene2Symbol
makeGene2symbolFromGFF	deprecated
makeGene2SymbolFromGTF	makeGene2Symbol
makeGene2symbolFromGTF	deprecated
makeGRanges	makeGRanges
makeGRangesFromEnsDb	makeGRanges
makeGRangesFromEnsembl	makeGRanges
makeGRangesFromGFF	makeGRanges
makeGRangesFromGTF	makeGRanges
makeNames	reexports
makeSampleData	makeSampleData
makeSingleCellExperiment	makeSingleCellExperiment
makeSummarizedExperiment	makeSummarizedExperiment
makeTx2Gene	makeTx2Gene
makeTx2GeneFromEnsDb	makeTx2Gene
makeTx2GeneFromEnsembl	makeTx2Gene
makeTx2geneFromEnsembl	deprecated
makeTx2GeneFromGFF	makeTx2Gene
makeTx2geneFromGFF	deprecated
makeTx2GeneFromGTF	makeTx2Gene
makeTx2geneFromGTF	deprecated
mapCellsToSamples	mapCellsToSamples
mapGenes	mapGenes
mapGenesToIDs,Gene2Symbol-method	mapGenes
mapGenesToIDs,SummarizedExperiment-method	mapGenes
mapGenesToRownames,Gene2Symbol-method	mapGenes
mapGenesToRownames,SummarizedExperiment-method	mapGenes
mapGenesToSymbols,Gene2Symbol-method	mapGenes
mapGenesToSymbols,SummarizedExperiment-method	mapGenes
markdown	markdown
markdown,SummarizedExperiment-method	markdown
markdownHeader	markdownHeader
markdownLink	markdownLink
markdownList	markdownList
markdownPlotlist	deprecated
markdownPlots	markdownPlots
markdownTables	markdownTables
mat	mat
matchArgsToDoCall	reexports
matchesGene2Symbol	matchesGene2Symbol
matchesInterestingGroups	matchesInterestingGroups
matchInterestingGroups	matchInterestingGroups
mdHeader	markdownHeader
mdLink	markdownLink
mdList	markdownList
mdPlotlist	deprecated
mdPlots	markdownPlots
mdTables	markdownTables
meltCounts	meltCounts
meltCounts,SummarizedExperiment-method	meltCounts
methodFormals	reexports
methodFunction	reexports
metrics	metrics
metrics,SingleCellExperiment-method	metrics
metrics,SummarizedExperiment-method	metrics
metricsPerSample,SingleCellExperiment-method	metrics
MGI2Ensembl	MGI2Ensembl-class
mgi2ensembl	deprecated
MGI2Ensembl-class	MGI2Ensembl-class
mgi2gene	deprecated
microplate	microplate
midnightTheme	defunct
minimalSampleData	minimalSampleData
multiassignAsEnvir	multiassignAsEnvir
multiassignAsNewEnvir	defunct
naStrings	reexports
organism	organism
organism,data.frame-method	organism
organism,DataFrame-method	organism
organism,GRanges-method	organism
organism,matrix-method	organism
organism,sparseMatrix-method	organism
organism,SummarizedExperiment-method	organism
organism_mappings	organism_mappings
PANTHER	PANTHER-class
panther	deprecated
PANTHER-class	PANTHER-class
paperwhiteTheme	defunct
params	params
parseGFFAttributes	defunct
pasteURL	reexports
plotCorrelationHeatmap	plotCorrelationHeatmap
plotCorrelationHeatmap,SingleCellExperiment-method	plotCorrelationHeatmap
plotCorrelationHeatmap,SummarizedExperiment-method	plotCorrelationHeatmap
plotCounts	plotCounts
plotCounts,SingleCellExperiment-method	defunct
plotCounts,SummarizedExperiment-method	plotCounts
plotCountsPerBiotype	plotCountsPerBiotype
plotCountsPerBiotype,SummarizedExperiment-method	plotCountsPerBiotype
plotCountsPerBroadClass	plotCountsPerBroadClass
plotCountsPerBroadClass,SummarizedExperiment-method	plotCountsPerBiotype
plotCountsPerGene	plotCountsPerGene
plotCountsPerGene,SingleCellExperiment-method	plotCountsPerGene
plotCountsPerGene,SummarizedExperiment-method	plotCountsPerGene
plotDEGHeatmap	reexports
plotDEGPCA	reexports
plotGenderMarkers	plotGenderMarkers
plotGenderMarkers,SingleCellExperiment-method	plotGenderMarkers
plotGenderMarkers,SummarizedExperiment-method	plotGenderMarkers
plotGene	reexports
plotGene,SummarizedExperiment-method	deprecated
plotGenesDetected	plotGenesDetected
plotGenesDetected,SingleCellExperiment-method	plotGenesDetected
plotGenesDetected,SummarizedExperiment-method	plotGenesDetected
plotHeatmap	plotHeatmap
plotHeatmap,SingleCellExperiment-method	plotHeatmap
plotHeatmap,SummarizedExperiment-method	plotHeatmap
plotPCA	plotPCA
plotPCA,SummarizedExperiment-method	plotPCA
plotQC	plotQC
plotQC,SummarizedExperiment-method	plotQC
plotQuantileHeatmap	plotQuantileHeatmap
plotQuantileHeatmap,SingleCellExperiment-method	plotQuantileHeatmap
plotQuantileHeatmap,SummarizedExperiment-method	plotQuantileHeatmap
plotTotalCounts	plotTotalCounts
plotTotalCounts,SingleCellExperiment-method	plotTotalCounts
plotTotalCounts,SummarizedExperiment-method	plotTotalCounts
plotZerosVsDepth	plotZerosVsDepth
plotZerosVsDepth,SummarizedExperiment-method	plotZerosVsDepth
prepareTemplate	prepareTemplate
printString	reexports
rdataExtPattern	reexports
rdataLoadError	reexports
readFileByExtension	deprecated
readGFF	deprecated
readGTF	deprecated
readJSON	deprecated
readYAML	deprecated
realpath	reexports
reexports	reexports
relevel	relevel
relevelColData	relevel
relevelRowRanges	relevel
removeNA	removeNA
removeNA,atomic-method	removeNA
removeNA,data.frame-method	removeNA
removeNA,DataFrame-method	removeNA
removeNA,matrix-method	removeNA
removeNA,sparseMatrix-method	removeNA
rse	rse
sampleData	sampleData
sampleData,SingleCellExperiment-method	sampleData
sampleData,SummarizedExperiment-method	sampleData
sampleData<-,SingleCellExperiment,DataFrame-method	sampleData
sampleData<-,SummarizedExperiment,DataFrame-method	sampleData
sampleNames	sampleNames
sampleNames,SummarizedExperiment-method	sampleData
sampleNames<-	sampleNames
sampleNames<-,SummarizedExperiment,character-method	sampleNames
sanitizeAnnotable	defunct
sanitizeColData	reexports
sanitizeNA	sanitizeNA
sanitizeNA,atomic-method	sanitizeNA
sanitizeNA,character-method	sanitizeNA
sanitizeNA,data.frame-method	sanitizeNA
sanitizeNA,DataFrame-method	sanitizeNA
sanitizeNA,factor-method	sanitizeNA
sanitizePercent	sanitizePercent
sanitizePercent,atomic-method	sanitizePercent
sanitizePercent,character-method	sanitizePercent
sanitizeRowData	reexports
sanitizeRowRanges	reexports
sanitizeSampleData	sanitizeSampleData
saveData	reexports
sce	sce
selectSamples	selectSamples
selectSamples,SingleCellExperiment-method	selectSamples
selectSamples,SummarizedExperiment-method	selectSamples
separator	separator
separatorBar	deprecated
setArgsToDoCall	defunct
show	show
show,EggNOG-method	show
show,PANTHER-method	show
showSlotInfo	showSlotInfo
snake	reexports
sortUnique	sortUnique
sparse	sparse
standardizeCall	reexports
stripTranscriptVersions	stripTranscriptVersions
stripTranscriptVersions,character-method	stripTranscriptVersions
stripTranscriptVersions,matrix-method	stripTranscriptVersions
stripTranscriptVersions,sparseMatrix-method	stripTranscriptVersions
stripTranscriptVersions,SummarizedExperiment-method	stripTranscriptVersions
subsetPerSample	subsetPerSample
subsetPerSample,SingleCellExperiment-method	subsetPerSample
summary	summary
summary,Gene2Symbol-method	summary
summary,Tx2Gene-method	summary
synonyms	defunct
tar	reexports
tbl	tbl
theme_midnight	ggplot2-themes
theme_paperwhite	ggplot2-themes
tibble	reexports
topCellsPerSample	topCellsPerSample
topCellsPerSample,SingleCellExperiment-method	topCellsPerSample
toStringUnique	toStringUnique
tpm	tpm
tpm,SummarizedExperiment-method	tpm
transmit	reexports
Tx2Gene	Tx2Gene-class
tx2gene	deprecated
Tx2Gene,DataFrame-method	Tx2Gene-class
Tx2Gene,GRanges-method	Tx2Gene-class
Tx2Gene,SummarizedExperiment-method	Tx2Gene-class
Tx2Gene-class	Tx2Gene-class
tx2geneFromGFF	defunct
tx2geneFromGTF	defunct
tx_se	tx_se
uniteInterestingGroups	uniteInterestingGroups
uniteInterestingGroups,data.frame-method	deprecated
uniteInterestingGroups,DataFrame-method	uniteInterestingGroups
untar	reexports
unzip	reexports
updateMessage	updateMessage
upperCamel	reexports
writeCounts	reexports
zerosVsDepth	zerosVsDepth
zerosVsDepth,matrix-method	zerosVsDepth
zerosVsDepth,SingleCellExperiment-method	zerosVsDepth
zerosVsDepth,sparseMatrix-method	zerosVsDepth
zerosVsDepth,SummarizedExperiment-method	zerosVsDepth
zip	reexports
