basejump-package	basejump-package
%$%	reexports
%<>%	reexports
%>%	reexports
%T>%	reexports
aggregate	aggregate
aggregateCellsToSamples	aggregateCellsToSamples
aggregateCellsToSamples,SingleCellExperiment-method	aggregateCellsToSamples
aggregateCols	aggregate
aggregateCols,matrix-method	aggregate
aggregateCols,SingleCellExperiment-method	aggregate
aggregateCols,sparseMatrix-method	aggregate
aggregateCols,SummarizedExperiment-method	aggregate
aggregateRows	aggregate
aggregateRows,matrix-method	aggregate
aggregateRows,sparseMatrix-method	aggregate
aggregateRows,SummarizedExperiment-method	aggregate
alphaThreshold	alphaThreshold
alphaThreshold,Annotated-method	alphaThreshold
alphaThreshold<-	alphaThreshold
alphaThreshold<-,Annotated,numeric-method	alphaThreshold
annotable	reexports
antiJoin	reexports
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,character-method	autopadZeros
autopadZeros,matrix-method	autopadZeros
autopadZeros,SummarizedExperiment-method	autopadZeros
barcodePattern	barcodePattern
basejump	basejump-package
basejumpTestsURL	basejumpTestsURL
basenameSansExt	reexports
bunzip2	reexports
bzip2	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,DataTable-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	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
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	convertGenesToSymbols
convertSymbolsToGenes,SummarizedExperiment-method	convertGenesToSymbols
convertTranscriptsToGenes	convertTranscriptsToGenes
convertTranscriptsToGenes,character-method	convertTranscriptsToGenes
convertTranscriptsToGenes,matrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,sparseMatrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,SummarizedExperiment-method	convertTranscriptsToGenes
convertUCSCBuildToEnsembl	reexports
counts	counts
counts,SummarizedExperiment-method	counts
counts<-	counts
counts<-,SummarizedExperiment,Matrix-method	counts
counts<-,SummarizedExperiment,matrix-method	counts
DataFrame	reexports
decode	reexports
decompressFile	reexports
defunct	defunct
deprecated	deprecated
detectHPC	detectHPC
detectLanes	detectLanes
detectOrganism	reexports
dots	reexports
dotted	reexports
dottedCase	dottedCase
dottedCase,atomic-method	dottedCase
dottedCase,data.frame-method	dottedCase
dottedCase,DataTable-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	reexports
encode	reexports
Ensembl2Entrez	Ensembl2Entrez
Ensembl2Entrez,DataFrame-method	Ensembl2Entrez
Ensembl2Entrez,GRanges-method	Ensembl2Entrez
Ensembl2Entrez,SummarizedExperiment-method	Ensembl2Entrez
Ensembl2Entrez-class	Ensembl2Entrez-class
ensemblVersion	genomeVersions
estimateSizeFactors	estimateSizeFactors
estimateSizeFactors,SingleCellExperiment-method	estimateSizeFactors
estimateSizeFactors,SummarizedExperiment-method	estimateSizeFactors
export	reexports
factorize	reexports
fileExt	reexports
filterCells	filterCells
filterCells,SingleCellExperiment-method	filterCells
flatFiles	reexports
flybaseVersion	genomeVersions
foldChangeToLogRatio	logRatio
foldChangeToLogRatio,numeric-method	logRatio
formalsList	formalsList
fullJoin	reexports
gencodeVersion	genomeVersions
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
genomeVersions	genomeVersions
geometricMean	geometricMean
geometricMean,matrix-method	geometricMean
geometricMean,numeric-method	geometricMean
geometricMean,sparseMatrix-method	geometricMean
getURL	reexports
getURLDirList	reexports
GRanges	reexports
GRangesList	reexports
gunzip	reexports
gzip	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
HGNC2Ensembl-class	HGNC2Ensembl-class
humanize	humanize
humanize,SummarizedExperiment-method	humanize
import	reexports
importSampleData	importSampleData
importTx2Gene	importTx2Gene
initDir	reexports
innerJoin	reexports
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
kebab	reexports
kebabCase	reexports
lanePattern	lanePattern
leftJoin	reexports
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	reexports
makeGRangesFromEnsembl	reexports
makeGRangesFromGFF	reexports
makeGRangesFromGTF	reexports
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
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
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
mutateAll	reexports
mutateAt	reexports
mutateIf	reexports
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,DataTable-method	organism
organism,GRanges-method	organism
organism,matrix-method	organism
organism,sparseMatrix-method	organism
organism,SummarizedExperiment-method	organism
organism<-	organism
organism<-,Annotated-method	organism
pasteURL	reexports
plotGene	reexports
prepareTemplate	prepareTemplate
printString	reexports
pseudobulk	pseudobulk
pseudobulk,SingleCellExperiment-method	pseudobulk
rankedMatrix	rankedMatrix
readFileByExtension	deprecated
readGFF	deprecated
readGTF	deprecated
readJSON	deprecated
readSampleData	deprecated
readTx2Gene	deprecated
readYAML	deprecated
realpath	reexports
reducedDims	reexports
reducedDims<-	reexports
reexports	reexports
refseqVersion	genomeVersions
relevel	reexports
relevelColData	defunct
relevelRowData	defunct
relevelRowRanges	defunct
removeNA	reexports
rightJoin	reexports
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
selectIf	reexports
selectSamples	selectSamples
selectSamples,SingleCellExperiment-method	selectSamples
selectSamples,SummarizedExperiment-method	selectSamples
semiJoin	reexports
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,DataTable-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,sparseMatrix-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	reexports
transmuteAt	reexports
transmuteIf	reexports
Tx2Gene	Tx2Gene
Tx2Gene,DataFrame-method	Tx2Gene
Tx2Gene,GRanges-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,DataTable-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
wormbaseVersion	genomeVersions
writeCounts	reexports
zerosVsDepth	zerosVsDepth
zerosVsDepth,matrix-method	zerosVsDepth
zerosVsDepth,SingleCellExperiment-method	zerosVsDepth
zerosVsDepth,sparseMatrix-method	zerosVsDepth
zerosVsDepth,SummarizedExperiment-method	zerosVsDepth
zip	reexports
