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
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,matrix-method	autopadZeros
autopadZeros,SummarizedExperiment-method	autopadZeros
barcodePattern	reexports
basejump	basejump-package
basejumpTestsURL	basejumpTestsURL
basenameSansExt	reexports
cacheURL	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
column_to_rownames	reexports
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
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	reexports
currentFlyBaseVersion	reexports
currentGencodeVersion	reexports
currentRefSeqVersion	reexports
currentWormBaseVersion	reexports
DataFrame	reexports
decode	reexports
decompress	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,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	reexports
encode	reexports
Ensembl2Entrez	reexports
Ensembl2Entrez-class	reexports-classes
Entrez2Ensembl	reexports
Entrez2Ensembl-class	reexports-classes
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	reexports
fullJoin	reexports
Gene2Symbol	reexports
Gene2Symbol-class	reexports-classes
geneNames	reexports
geneSynonyms	reexports
genomeMetadataNames	reexports
geometricMean	geometricMean
geometricMean,Matrix-method	geometricMean
geometricMean,matrix-method	geometricMean
geometricMean,numeric-method	geometricMean
getEnsDb	reexports
getURLDirList	reexports
GRanges	reexports
GRangesList	reexports
headtail	headtail
headtail,DataFrame-method	headtail
headtail,GRanges-method	headtail
headtail,Matrix-method	headtail
headtail,SummarizedExperiment-method	headtail
HGNC	reexports
HGNC-class	reexports-classes
HGNC2Ensembl	reexports
HGNC2Ensembl-class	reexports-classes
humanize	humanize
humanize,SummarizedExperiment-method	humanize
import	reexports
importSampleData	importSampleData
importTx2Gene	reexports
initDir	reexports
innerJoin	reexports
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
intersectAll	intersectAll
intersectAll,list-method	intersectAll
intersectionMatrix	intersectionMatrix
intersectionMatrix,list-method	intersectionMatrix
IRanges	reexports
kebab	reexports
kebabCase	reexports
lanePattern	reexports
leftJoin	reexports
loadData	reexports
loadDataAsName	reexports
loadRemoteData	reexports
localOrRemoteFile	reexports
logRatio	logRatio
logRatioToFoldChange	logRatio
logRatioToFoldChange,numeric-method	logRatio
makeDimnames	reexports
makeGene2SymbolFromEnsDb	reexports
makeGene2SymbolFromEnsembl	reexports
makeGene2SymbolFromGFF	reexports
makeGene2SymbolFromGTF	reexports
makeGRangesFromEnsDb	reexports
makeGRangesFromEnsembl	reexports
makeGRangesFromGFF	reexports
makeGRangesFromGTF	reexports
makeLabel	reexports
makeNames	reexports
makeProtein2GeneFromEnsembl	reexports
makeSampleData	makeSampleData
makeSampleData,data.frame-method	makeSampleData
makeSampleData,DataFrame-method	makeSampleData
makeSingleCellExperiment	makeSingleCellExperiment
makeSummarizedExperiment	makeSummarizedExperiment
makeTitle	reexports
makeTx2GeneFromEnsDb	reexports
makeTx2GeneFromEnsembl	reexports
makeTx2GeneFromFASTA	reexports
makeTx2GeneFromGFF	reexports
makeTx2GeneFromGTF	reexports
makeWords	reexports
mapCellsToSamples	mapCellsToSamples
mapEnsemblReleaseToURL	reexports
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
mapHumanOrthologs	reexports
mapUCSCBuildToEnsembl	reexports
markdown	markdown
markdown,SummarizedExperiment-method	markdown
markdownHeader	markdownHeader
markdownLink	markdownLink
markdownList	markdownList
markdownPlots	markdownPlots
markdownTables	markdownTables
matchArgsToDoCall	reexports
matchEnsemblReleaseToURL	deprecated
matchesGene2Symbol	matchesGene2Symbol
matchesInterestingGroups	matchesInterestingGroups
matchHumanOrthologs	deprecated
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,Matrix-method	melt
melt,SingleCellExperiment-method	melt
melt,SummarizedExperiment-method	melt
metadata	reexports
metadata2	reexports
metadata2<-	reexports
metadata<-	reexports
metadataBlacklist	reexports
methodFormals	reexports
methodFunction	reexports
metrics	metrics
metrics,SingleCellExperiment-method	metrics
metrics,SummarizedExperiment-method	metrics
metricsCols	reexports
metricsPerSample	metrics
metricsPerSample,SingleCellExperiment-method	metrics
MGI2Ensembl	reexports
MGI2Ensembl-class	reexports-classes
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	reexports
organism<-	reexports
pasteURL	reexports
prepareTemplate	prepareTemplate
printString	reexports
Protein2Gene-class	reexports-classes
rankedMatrix	rankedMatrix
readFileByExtension	deprecated
readGFF	deprecated
readGTF	deprecated
readJSON	deprecated
readSampleData	deprecated
readTx2Gene	deprecated
readYAML	deprecated
realpath	reexports
reducedDims	reexports
reducedDims<-	reexports
reexports	reexports
reexports-classes	reexports-classes
relevelColData	defunct
relevelRowData	defunct
relevelRowRanges	defunct
removeNA	reexports
requireNamespaces	reexports
rightJoin	reexports
rowData	reexports
rowData<-	reexports
rownames_to_column	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
sem	sem
sem,AsIs-method	sem
semiJoin	reexports
separator	separator
separatorBar	defunct
showHeader	showHeader
showSlotInfo	reexports
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
splitByLevel	reexports
standardizeCall	reexports
stripGeneVersions	reexports
stripTranscriptVersions	reexports
subsetPerSample	subsetPerSample
subsetPerSample,SingleCellExperiment-method	subsetPerSample
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	reexports
Tx2Gene-class	reexports-classes
tx2geneFromGFF	defunct
uniteInterestingGroups	uniteInterestingGroups
uniteInterestingGroups,data.frame-method	deprecated
uniteInterestingGroups,DataFrame-method	uniteInterestingGroups
updateMessage	reexports
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
