basejump-package	basejump-package
%$%	reexports
%<>%	reexports
%>%	reexports
%T>%	reexports
aggregate	aggregate
aggregate,Matrix-method	aggregate
aggregate,matrix-method	aggregate
aggregateCellsToSamples	aggregateCellsToSamples
aggregateCellsToSamples,SingleCellExperiment-method	aggregateCellsToSamples
aggregateCols	aggregateCols
aggregateCols,Matrix-method	aggregateCols
aggregateCols,matrix-method	aggregateCols
aggregateCols,SingleCellExperiment-method	aggregateCols
aggregateCols,SummarizedExperiment-method	aggregateCols
aggregateRows	aggregateRows
aggregateRows,Matrix-method	aggregateRows
aggregateRows,matrix-method	aggregateRows
aggregateRows,SummarizedExperiment-method	aggregateRows
alphaThreshold	alphaThreshold
alphaThreshold,Annotated-method	alphaThreshold
alphaThreshold<-	alphaThreshold
alphaThreshold<-,Annotated,numeric-method	alphaThreshold
annotable	makeGRangesFromEnsembl
antiJoin	join
antiJoin,DataFrame,DataFrame,character-method	join
as.data.frame	reexports
as.data.table	reexports
as.SummarizedExperiment	reexports
assay	reexports
assay<-	reexports
assayNames	reexports
assays	reexports
assays<-	reexports
assignAndSaveData	reexports
as_tibble	reexports
atomize	reexports
autopadZeros	autopadZeros
autopadZeros,matrix-method	autopadZeros
autopadZeros,SummarizedExperiment-method	autopadZeros
barcodePattern	barcodePattern
basejump	basejump-package
basejumpTestsURL	basejumpTestsURL
basenameSansExt	reexports
calculateMetrics	calculateMetrics
calculateMetrics,Matrix-method	calculateMetrics
calculateMetrics,matrix-method	calculateMetrics
calculateMetrics,RangedSummarizedExperiment-method	calculateMetrics
calculateMetrics,SingleCellExperiment-method	calculateMetrics
camel	reexports
camelCase	camelCase
camelCase,atomic-method	camelCase
camelCase,data.frame-method	camelCase
camelCase,DataFrame-method	camelCase
camelCase,factor-method	camelCase
camelCase,list-method	camelCase
camelCase,Matrix-method	camelCase
camelCase,matrix-method	camelCase
camelCase,Ranges-method	camelCase
camelCase,SummarizedExperiment-method	camelCase
camelCase,Vector-method	camelCase
capitalize	reexports
cell2sample	cell2sample
cell2sample,SingleCellExperiment-method	cell2sample
coerceS4ToList	deprecated
coerceToList	reexports
colData	reexports
colData<-	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
compress	reexports
compressExtPattern	reexports
convertGenesToSymbols	convertGenesToSymbols
convertGenesToSymbols,character-method	convertGenesToSymbols
convertGenesToSymbols,GRanges-method	convertGenesToSymbols
convertGenesToSymbols,Matrix-method	convertGenesToSymbols
convertGenesToSymbols,matrix-method	convertGenesToSymbols
convertGenesToSymbols,SummarizedExperiment-method	convertGenesToSymbols
convertSampleIDsToNames	convertSampleIDsToNames
convertSampleIDsToNames,SingleCellExperiment-method	convertSampleIDsToNames
convertSampleIDsToNames,SummarizedExperiment-method	convertSampleIDsToNames
convertSymbolsToGenes	convertGenesToSymbols
convertSymbolsToGenes,SummarizedExperiment-method	convertGenesToSymbols
convertTranscriptsToGenes	convertTranscriptsToGenes
convertTranscriptsToGenes,character-method	convertTranscriptsToGenes
convertTranscriptsToGenes,Matrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,matrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,SummarizedExperiment-method	convertTranscriptsToGenes
convertUCSCBuildToEnsembl	convertUCSCBuildToEnsembl
correlation	correlation
correlation,Matrix,Matrix-method	correlation
correlation,matrix,matrix-method	correlation
correlation,Matrix,missingOrNULL-method	correlation
correlation,matrix,missingOrNULL-method	correlation
correlation,numeric,numeric-method	correlation
correlation,SummarizedExperiment,missingOrNULL-method	correlation
correlation,SummarizedExperiment,SummarizedExperiment-method	correlation
counts	counts
counts,SummarizedExperiment-method	counts
counts<-	counts
counts<-,SummarizedExperiment,Matrix-method	counts
counts<-,SummarizedExperiment,matrix-method	counts
currentEnsemblVersion	currentGenomeVersion
currentFlybaseVersion	currentGenomeVersion
currentGencodeVersion	currentGenomeVersion
currentGenomeVersion	currentGenomeVersion
currentRefseqVersion	currentGenomeVersion
currentWormbaseVersion	currentGenomeVersion
DataFrame	reexports
decode	reexports
decompress	reexports
defunct	defunct
deprecated	deprecated
detectHPC	detectHPC
detectLanes	detectLanes
detectOrganism	detectOrganism
dots	reexports
dotted	reexports
dottedCase	dottedCase
dottedCase,atomic-method	dottedCase
dottedCase,data.frame-method	dottedCase
dottedCase,DataFrame-method	dottedCase
dottedCase,factor-method	dottedCase
dottedCase,list-method	dottedCase
dottedCase,Matrix-method	dottedCase
dottedCase,matrix-method	dottedCase
dottedCase,Ranges-method	dottedCase
dottedCase,SummarizedExperiment-method	dottedCase
dottedCase,Vector-method	dottedCase
emptyRanges	emptyRanges
encode	reexports
Ensembl2Entrez	Ensembl2Entrez
Ensembl2Entrez,DataFrame-method	Ensembl2Entrez
Ensembl2Entrez,GRanges-method	Ensembl2Entrez
Ensembl2Entrez,SummarizedExperiment-method	Ensembl2Entrez
Ensembl2Entrez-class	Ensembl2Entrez-class
estimateSizeFactors	estimateSizeFactors
estimateSizeFactors,SingleCellExperiment-method	estimateSizeFactors
estimateSizeFactors,SummarizedExperiment-method	estimateSizeFactors
export	reexports
extPattern	reexports
factorize	reexports
fileExt	reexports
filterCells	filterCells
filterCells,SingleCellExperiment-method	filterCells
flatFiles	defunct
flatFiles,SummarizedExperiment-method	defunct
foldChangeToLogRatio	logRatio
foldChangeToLogRatio,numeric-method	logRatio
formalsList	formalsList
fullJoin	join
fullJoin,DataFrame,DataFrame,character-method	join
Gene2Symbol	Gene2Symbol
Gene2Symbol,DataFrame-method	Gene2Symbol
Gene2Symbol,GRanges-method	Gene2Symbol
Gene2Symbol,SummarizedExperiment-method	Gene2Symbol
Gene2Symbol-class	Gene2Symbol-class
geneNames	geneNames
geneNames,GRanges-method	geneNames
geneNames,SummarizedExperiment-method	geneNames
geneSynonyms	geneSynonyms
genomeMetadataNames	genomeMetadataNames
geometricMean	geometricMean
geometricMean,Matrix-method	geometricMean
geometricMean,matrix-method	geometricMean
geometricMean,numeric-method	geometricMean
getURL	reexports
getURLDirList	getURLDirList
GRanges	reexports
GRangesList	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,matrix-method	headtail
headtail,SummarizedExperiment-method	headtail
HGNC2Ensembl	HGNC2Ensembl
HGNC2Ensembl-class	HGNC2Ensembl-class
humanize	humanize
humanize,SummarizedExperiment-method	humanize
import	reexports
importSampleData	importSampleData
importTx2Gene	importTx2Gene
initDir	reexports
innerJoin	join
innerJoin,DataFrame,DataFrame,character-method	join
integerCounts	integerCounts
integerCounts,Matrix-method	integerCounts
integerCounts,matrix-method	integerCounts
integerCounts,SummarizedExperiment-method	integerCounts
interestingGroups	interestingGroups
interestingGroups,Annotated-method	interestingGroups
interestingGroups<-	interestingGroups
interestingGroups<-,Annotated,character-method	interestingGroups
interestingGroups<-,Annotated,NULL-method	interestingGroups
interestingGroups<-,SummarizedExperiment,character-method	interestingGroups
IRanges	reexports
join	join
kebab	reexports
kebabCase	reexports
lanePattern	lanePattern
leftJoin	join
leftJoin,DataFrame,DataFrame,character-method	join
lfcThreshold	lfcThreshold
lfcThreshold,Annotated-method	lfcThreshold
lfcThreshold<-	lfcThreshold
lfcThreshold<-,Annotated,numeric-method	lfcThreshold
loadData	reexports
loadDataAsName	reexports
loadRemoteData	reexports
localOrRemoteFile	reexports
logRatio	logRatio
logRatioToFoldChange	logRatio
logRatioToFoldChange,numeric-method	logRatio
makeDimnames	reexports
makeGene2Symbol	makeGene2Symbol
makeGene2SymbolFromEnsDb	makeGene2Symbol
makeGene2SymbolFromEnsembl	makeGene2Symbol
makeGene2SymbolFromGFF	makeGene2Symbol
makeGene2SymbolFromGTF	makeGene2Symbol
makeGRangesFromEnsDb	makeGRangesFromEnsDb
makeGRangesFromEnsembl	makeGRangesFromEnsembl
makeGRangesFromGFF	makeGRangesFromGFF
makeGRangesFromGTF	makeGRangesFromGFF
makeLabel	reexports
makeNames	reexports
makeSampleData	makeSampleData
makeSampleData,data.frame-method	makeSampleData
makeSampleData,DataFrame-method	makeSampleData
makeSingleCellExperiment	makeSingleCellExperiment
makeSingleCellExperiment,list-method	makeSingleCellExperiment
makeSingleCellExperiment,SimpleList-method	makeSingleCellExperiment
makeSummarizedExperiment	makeSummarizedExperiment
makeSummarizedExperiment,list-method	makeSummarizedExperiment
makeSummarizedExperiment,SimpleList-method	makeSummarizedExperiment
makeTitle	reexports
makeTx2Gene	makeTx2Gene
makeTx2GeneFromEnsDb	makeTx2Gene
makeTx2GeneFromEnsembl	makeTx2Gene
makeTx2GeneFromFASTA	makeTx2GeneFromFASTA
makeTx2GeneFromGFF	makeTx2Gene
makeTx2GeneFromGTF	makeTx2Gene
makeWords	reexports
mapCellsToSamples	mapCellsToSamples
mapGenes	mapGenes
mapGenesToIDs	mapGenes
mapGenesToIDs,Gene2Symbol-method	mapGenes
mapGenesToIDs,SummarizedExperiment-method	mapGenes
mapGenesToRownames	mapGenes
mapGenesToRownames,Gene2Symbol-method	mapGenes
mapGenesToRownames,SummarizedExperiment-method	mapGenes
mapGenesToSymbols	mapGenes
mapGenesToSymbols,Gene2Symbol-method	mapGenes
mapGenesToSymbols,SummarizedExperiment-method	mapGenes
markdown	markdown
markdown,SummarizedExperiment-method	markdown
markdownHeader	markdownHeader
markdownLink	markdownLink
markdownList	markdownList
markdownPlots	markdownPlots
markdownTables	markdownTables
matchArgsToDoCall	reexports
matchEnsemblReleaseToURL	matchEnsemblReleaseToURL
matchesGene2Symbol	matchesGene2Symbol
matchesInterestingGroups	matchesInterestingGroups
matchHumanOrthologs	matchHumanOrthologs
matchInterestingGroups	matchInterestingGroups
mcolnames	mcolnames
mcolnames,Vector-method	mcolnames
mcolnames<-	mcolnames
mcolnames<-,Vector,character-method	mcolnames
mcols	reexports
mcols<-	reexports
mdHeader	markdownHeader
mdLink	markdownLink
mdList	markdownList
mdPlots	markdownPlots
mdTables	markdownTables
melt	melt
melt,DataFrame-method	melt
melt,Matrix-method	melt
melt,matrix-method	melt
melt,SingleCellExperiment-method	melt
melt,SummarizedExperiment-method	melt
melt,table-method	melt
metadata	reexports
metadata2	reexports
metadata2<-	reexports
metadata<-	reexports
metadataBlacklist	metadataBlacklist
methodFormals	reexports
methodFunction	reexports
metrics	metrics
metrics,SingleCellExperiment-method	metrics
metrics,SummarizedExperiment-method	metrics
metricsCols	metricsCols
metricsPerSample	metrics
metricsPerSample,SingleCellExperiment-method	metrics
MGI2Ensembl	MGI2Ensembl
MGI2Ensembl-class	MGI2Ensembl-class
microplate	microplate
minimalSampleData	minimalSampleData
multiassignAsEnvir	multiassignAsEnvir
mutate	mutate
mutateAll	mutate
mutateAll,DataFrame,function-method	mutate
mutateAt	mutate
mutateAt,DataFrame,character,function-method	mutate
mutateIf	mutate
mutateIf,DataFrame,function,function-method	mutate
naStrings	reexports
nonzeroRowsAndCols	nonzeroRowsAndCols
nonzeroRowsAndCols,Matrix-method	nonzeroRowsAndCols
nonzeroRowsAndCols,matrix-method	nonzeroRowsAndCols
nonzeroRowsAndCols,SummarizedExperiment-method	nonzeroRowsAndCols
organism	organism
organism,Annotated-method	organism
organism,data.frame-method	organism
organism,DataFrame-method	organism
organism,GRanges-method	organism
organism,Matrix-method	organism
organism,matrix-method	organism
organism,SummarizedExperiment-method	organism
organism<-	organism
organism<-,Annotated-method	organism
pasteURL	reexports
plotGene	reexports
prepareTemplate	prepareTemplate
printString	reexports
rankedMatrix	rankedMatrix
readFileByExtension	deprecated
readGFF	deprecated
readGTF	deprecated
readJSON	deprecated
readSampleData	deprecated
readTx2Gene	deprecated
readYAML	deprecated
realpath	reexports
reducedDims	reexports
reducedDims<-	reexports
reexports	reexports
relevelColData	defunct
relevelRowData	defunct
relevelRowRanges	defunct
removeNA	reexports
rightJoin	join
rightJoin,DataFrame,DataFrame,character-method	join
rowData	reexports
rowData<-	reexports
rowRanges	reexports
rowRanges<-	reexports
sampleData	sampleData
sampleData,SingleCellExperiment-method	sampleData
sampleData,SummarizedExperiment-method	sampleData
sampleData<-	sampleData
sampleData<-,SingleCellExperiment,DataFrame-method	sampleData
sampleData<-,SummarizedExperiment,DataFrame-method	sampleData
sampleNames	sampleNames
sampleNames,SummarizedExperiment-method	sampleData
sampleNames<-	sampleNames
sampleNames<-,SummarizedExperiment,character-method	sampleNames
sanitizeNA	reexports
sanitizePercent	reexports
sanitizeSampleData	sanitizeSampleData
saveData	reexports
select	select
selectIf	select
selectIf,DataFrame,function-method	select
selectSamples	selectSamples
selectSamples,SingleCellExperiment-method	selectSamples
selectSamples,SummarizedExperiment-method	selectSamples
semiJoin	join
semiJoin,DataFrame,DataFrame,character-method	join
separator	separator
separatorBar	defunct
showHeader	showHeader
showSlotInfo	showSlotInfo
SimpleList	reexports
sizeFactors	sizeFactors
sizeFactors,SummarizedExperiment-method	sizeFactors
sizeFactors<-	sizeFactors
sizeFactors<-,SummarizedExperiment-method	sizeFactors
snake	reexports
snakeCase	snakeCase
snakeCase,atomic-method	snakeCase
snakeCase,data.frame-method	snakeCase
snakeCase,DataFrame-method	snakeCase
snakeCase,factor-method	snakeCase
snakeCase,list-method	snakeCase
snakeCase,Matrix-method	snakeCase
snakeCase,matrix-method	snakeCase
snakeCase,Ranges-method	snakeCase
snakeCase,SummarizedExperiment-method	snakeCase
snakeCase,Vector-method	snakeCase
sortUnique	sortUnique
standardizeCall	reexports
stripGeneVersions	stripTranscriptVersions
stripTranscriptVersions	stripTranscriptVersions
stripTranscriptVersions,character-method	stripTranscriptVersions
stripTranscriptVersions,Matrix-method	stripTranscriptVersions
stripTranscriptVersions,matrix-method	stripTranscriptVersions
stripTranscriptVersions,SummarizedExperiment-method	stripTranscriptVersions
subsetPerSample	subsetPerSample
subsetPerSample,SingleCellExperiment-method	subsetPerSample
summary	summary
summary,Gene2Symbol-method	summary
summary,Tx2Gene-method	summary
tar	reexports
theme_midnight	defunct
theme_paperwhite	defunct
tibble	reexports
topCellsPerSample	topCellsPerSample
topCellsPerSample,SingleCellExperiment-method	topCellsPerSample
toStringUnique	toStringUnique
tpm	tpm
tpm,SummarizedExperiment-method	tpm
transmit	transmit
transmuteAt	mutate
transmuteAt,DataFrame,character,function-method	mutate
transmuteIf	mutate
transmuteIf,DataFrame,function,function-method	mutate
Tx2Gene	Tx2Gene
Tx2Gene,data.frame-method	Tx2Gene
Tx2Gene,DataFrame-method	Tx2Gene
Tx2Gene,GRanges-method	Tx2Gene
Tx2Gene,matrix-method	Tx2Gene
Tx2Gene,SummarizedExperiment-method	Tx2Gene
Tx2Gene-class	Tx2Gene-class
tx2geneFromGFF	defunct
uniteInterestingGroups	uniteInterestingGroups
uniteInterestingGroups,data.frame-method	deprecated
uniteInterestingGroups,DataFrame-method	uniteInterestingGroups
untar	reexports
unzip	reexports
updateMessage	updateMessage
upperCamel	reexports
upperCamelCase	upperCamelCase
upperCamelCase,atomic-method	upperCamelCase
upperCamelCase,data.frame-method	upperCamelCase
upperCamelCase,DataFrame-method	upperCamelCase
upperCamelCase,factor-method	upperCamelCase
upperCamelCase,list-method	upperCamelCase
upperCamelCase,Matrix-method	upperCamelCase
upperCamelCase,matrix-method	upperCamelCase
upperCamelCase,Ranges-method	upperCamelCase
upperCamelCase,SummarizedExperiment-method	upperCamelCase
upperCamelCase,Vector-method	upperCamelCase
zerosVsDepth	zerosVsDepth
zerosVsDepth,Matrix-method	zerosVsDepth
zerosVsDepth,matrix-method	zerosVsDepth
zerosVsDepth,SingleCellExperiment-method	zerosVsDepth
zerosVsDepth,SummarizedExperiment-method	zerosVsDepth
zip	reexports
