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
aggregateFeatures	defunct
aggregateReplicates	defunct
aggregateRows	aggregate
aggregateRows,matrix-method	aggregate
aggregateRows,sparseMatrix-method	aggregate
aggregateRows,SummarizedExperiment-method	aggregate
aggregateSamples	defunct
alphaThreshold	alphaThreshold
alphaThreshold,Annotated-method	alphaThreshold
alphaThreshold<-	alphaThreshold
alphaThreshold<-,Annotated,numeric-method	alphaThreshold
annotable	reexports
as.data.frame	reexports-S4
as.data.table	reexports
as.SummarizedExperiment	reexports
assay	reexports
assay<-	reexports
assayNames	reexports
assays	reexports
assays<-	reexports
assert	reexports
assertAreGeneAnnotations	deprecated
assertFormalGene2symbol	deprecated
assertFormalInterestingGroups	deprecated
assertHasRownames	defunct
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-S4
autopadZeros	autopadZeros
autopadZeros,character-method	autopadZeros
autopadZeros,matrix-method	autopadZeros
autopadZeros,SummarizedExperiment-method	autopadZeros
barcodePattern	barcodePattern
basejump	basejump-package
basejumpTestsURL	basejumpTestsURL
basenameSansExt	reexports
broadClass	defunct
bunzip2	reexports
bzip2	reexports
calculateMetrics	calculateMetrics
calculateMetrics,DelayedArray-method	calculateMetrics
calculateMetrics,Matrix-method	calculateMetrics
calculateMetrics,matrix-method	calculateMetrics
calculateMetrics,RangedSummarizedExperiment-method	calculateMetrics
calculateMetrics,SingleCellExperiment-method	calculateMetrics
camel	reexports
camelCase	reexports-S4
capitalize	reexports-S4
cell2sample	cell2sample
cell2sample,SingleCellExperiment-method	cell2sample
checkClasses	defunct
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-S4
decompressFile	reexports
defunct	defunct
deprecated	deprecated
detectHPC	detectHPC
detectLanes	detectLanes
detectOrganism	reexports
dots	reexports
dotted	reexports
dottedCase	reexports-S4
EggNOG	EggNOG
eggnog	defunct
EggNOG-class	EggNOG-class
emptyRanges	reexports
encode	reexports-S4
Ensembl2Entrez	Ensembl2Entrez
ensembl2entrez	defunct
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-S4
extPattern	reexports
factorize	reexports-S4
fileExt	reexports
filterCells	filterCells
filterCells,SingleCellExperiment-method	filterCells
fixNA	deprecated
flatFiles	reexports-S4
foldChangeToLogRatio	logRatio
foldChangeToLogRatio,numeric-method	logRatio
formalsList	formalsList
Gene2Symbol	Gene2Symbol
gene2symbol	defunct
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,numeric-method	geometricMean
geometricMean,sparseMatrix-method	geometricMean
GRanges	reexports
GRangesList	reexports
grepString	defunct
gunzip	reexports
gzip	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
hgnc2ensembl	defunct
HGNC2Ensembl-class	HGNC2Ensembl-class
hgnc2gene	defunct
humanize	humanize
humanize,SummarizedExperiment-method	humanize
import	reexports
initDir	reexports
initializeDirectory	deprecated
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
kables	deprecated
kebab	reexports
kebabCase	reexports-S4
lanePattern	lanePattern
left_join	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
makeGene2symbolFromEnsembl	defunct
makeGene2SymbolFromGFF	makeGene2Symbol
makeGene2symbolFromGFF	defunct
makeGene2SymbolFromGTF	makeGene2Symbol
makeGene2symbolFromGTF	defunct
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
makeTx2geneFromEnsembl	defunct
makeTx2GeneFromGFF	makeTx2Gene
makeTx2geneFromGFF	defunct
makeTx2GeneFromGTF	makeTx2Gene
makeTx2geneFromGTF	defunct
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
markdownPlotlist	deprecated
markdownPlots	markdownPlots
markdownTables	markdownTables
matchArgsToDoCall	reexports
matchEnsemblReleaseToURL	matchEnsemblReleaseToURL
matchesGene2Symbol	matchesGene2Symbol
matchesInterestingGroups	matchesInterestingGroups
matchHumanOrthologs	matchHumanOrthologs
matchInterestingGroups	matchInterestingGroups
mcolnames	reexports-S4
mcolnames<-	reexports-S4
mcols	reexports
mcols<-	reexports
mdHeader	markdownHeader
mdLink	markdownLink
mdList	markdownList
mdPlotlist	deprecated
mdPlots	markdownPlots
mdTables	markdownTables
meltCounts	meltCounts
meltCounts,matrix-method	meltCounts
meltCounts,SummarizedExperiment-method	meltCounts
metadata	reexports
metadata<-	reexports
metadataBlacklist	metadataBlacklist
methodFormals	reexports
methodFunction	reexports
metrics	metrics
metrics,SingleCellExperiment-method	metrics
metrics,SummarizedExperiment-method	metrics
metricsPerSample	metrics
metricsPerSample,SingleCellExperiment-method	metrics
MGI2Ensembl	MGI2Ensembl
mgi2ensembl	defunct
MGI2Ensembl-class	MGI2Ensembl-class
mgi2gene	defunct
microplate	microplate
minimalSampleData	minimalSampleData
multiassignAsEnvir	multiassignAsEnvir
naStrings	reexports
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
PANTHER	PANTHER
panther	defunct
PANTHER-class	PANTHER-class
pasteURL	reexports
plotDEGHeatmap	reexports-S4
plotDEGPCA	reexports-S4
plotGene	reexports
prepareTemplate	prepareTemplate
printString	reexports
pseudobulk	pseudobulk
pseudobulk,SingleCellExperiment-method	pseudobulk
rankedMatrix	rankedMatrix
rdataExtPattern	reexports
readFileByExtension	deprecated
readGFF	deprecated
readGTF	deprecated
readJSON	deprecated
readYAML	deprecated
realpath	reexports
reducedDims	reexports
reducedDims<-	reexports
reexports	reexports
reexports-S4	reexports-S4
relevel	reexports
relevelColData	deprecated
relevelRowData	deprecated
relevelRowRanges	deprecated
removeNA	reexports-S4
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
sanitizeColData	reexports
sanitizeNA	reexports-S4
sanitizePercent	reexports-S4
sanitizeRowData	reexports
sanitizeRowRanges	reexports
sanitizeSampleData	sanitizeSampleData
saveData	reexports
selectSamples	selectSamples
selectSamples,SingleCellExperiment-method	selectSamples
selectSamples,SummarizedExperiment-method	selectSamples
separator	separator
separatorBar	deprecated
setArgsToDoCall	defunct
set_colnames	reexports
set_names	reexports
set_rownames	reexports
show	show
show,EggNOG-method	show
show,PANTHER-method	show
showHeader	showHeader
showSlotInfo	showSlotInfo
SimpleList	reexports
sizeFactors	sizeFactors
sizeFactors,SummarizedExperiment-method	sizeFactors
sizeFactors<-	sizeFactors
sizeFactors<-,SummarizedExperiment-method	sizeFactors
snake	reexports
snakeCase	reexports-S4
sortUnique	sortUnique
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
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
Tx2Gene	Tx2Gene
tx2gene	defunct
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	reexports-S4
writeCounts	reexports
zerosVsDepth	zerosVsDepth
zerosVsDepth,matrix-method	zerosVsDepth
zerosVsDepth,SingleCellExperiment-method	zerosVsDepth
zerosVsDepth,sparseMatrix-method	zerosVsDepth
zerosVsDepth,SummarizedExperiment-method	zerosVsDepth
zip	reexports
