basejump-package	basejump-package
%>%	reexports
aggregateFeatures	aggregateFeatures
aggregateFeatures,dgCMatrix-method	aggregateFeatures
aggregateFeatures,matrix-method	aggregateFeatures
aggregateReplicates	aggregateReplicates
aggregateReplicates,dgCMatrix-method	aggregateReplicates
aggregateReplicates,matrix-method	aggregateReplicates
annotable	annotable
assert	assert
assertAllAreNonExisting	assertAllAreNonExisting
assertAreGeneAnnotations	assertAreGeneAnnotations
assertAreTranscriptAnnotations	assertAreTranscriptAnnotations
assertFormalColorFunction	deprecated
assertFormalCompress	assertFormalCompress
assertFormalGene2symbol	assertFormalGene2symbol
assertFormalHeaderLevel	deprecated
assertHasRownames	assertHasRownames
assertIsAHeaderLevel	assertIsAHeaderLevel
assertIsAnImplicitInteger	assertIsImplicitInteger
assertIsAnImplicitIntegerOrNULL	assertIsImplicitInteger
assertIsAnIntegerOrNULL	assertIsAnIntegerOrNULL
assertIsAnnotable	deprecated
assertIsANumberOrNULL	assertIsANumberOrNULL
assertIsAStringOrNULL	assertIsAStringOrNULL
assertIsCharacterOrNULL	assertIsCharacterOrNULL
assertIsColorScaleContinuousOrNULL	assertIsColorScaleContinuousOrNULL
assertIsColorScaleDiscreteOrNULL	assertIsColorScaleDiscreteOrNULL
assertIsDataFrameOrNULL	assertIsDataFrameOrNULL
assertIsFillScaleContinuousOrNULL	assertIsFillScaleContinuousOrNULL
assertIsFillScaleDiscreteOrNULL	assertIsFillScaleDiscreteOrNULL
assertIsGene2symbol	assertIsGene2symbol
assertIsGFF	assertIsGFF
assertIsHexColorFunctionOrNULL	assertIsHexColorFunctionOrNULL
assertIsImplicitInteger	assertIsImplicitInteger
assertIsImplicitIntegerOrNULL	assertIsImplicitInteger
assertIsTx2gene	assertIsTx2gene
assertIsURL	assertIsURL
assignAndSaveData	assignAndSaveData
basejump	basejump-package
broadClass	broadClass
broadClass,data.frame-method	broadClass
broadClass,DataFrame-method	broadClass
broadClass,GRanges-method	broadClass
camel	makeNames
camel,ANY-method	makeNames
camel,character-method	makeNames
camel,data.frame-method	makeNames
camel,DataFrame-method	makeNames
camel,factor-method	makeNames
camel,GRanges-method	makeNames
camel,List-method	makeNames
camel,list-method	makeNames
camel,matrix-method	makeNames
camel,SimpleList-method	makeNames
checkAnnotable	deprecated
checkGene2symbol	deprecated
checkTx2gene	deprecated
coerce-tibble	coerce-tibble
collapseToString	collapseToString
collapseToString,atomic-method	collapseToString
collapseToString,data.frame-method	collapseToString
collapseToString,DataFrame-method	collapseToString
collapseToString,matrix-method	collapseToString
comp	deprecated
convertGenesToSymbols	convertGenesToSymbols
convertGenesToSymbols,character-method	convertGenesToSymbols
convertGenesToSymbols,data.frame-method	convertGenesToSymbols
convertGenesToSymbols,DataFrame-method	convertGenesToSymbols
convertGenesToSymbols,dgCMatrix-method	convertGenesToSymbols
convertGenesToSymbols,dgTMatrix-method	convertGenesToSymbols
convertGenesToSymbols,matrix-method	convertGenesToSymbols
convertTranscriptsToGenes	convertTranscriptsToGenes
convertTranscriptsToGenes,character-method	convertTranscriptsToGenes
convertTranscriptsToGenes,data.frame-method	convertTranscriptsToGenes
convertTranscriptsToGenes,DataFrame-method	convertTranscriptsToGenes
convertTranscriptsToGenes,dgCMatrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,dgTMatrix-method	convertTranscriptsToGenes
convertTranscriptsToGenes,matrix-method	convertTranscriptsToGenes
convertUCSCBuildToEnsembl	convertUCSCBuildToEnsembl
DataFrame	reexports
deprecated	deprecated
detectHPC	detectHPC
detectOrganism	detectOrganism
detectOrganism,character-method	detectOrganism
detectOrganism,data.frame-method	detectOrganism
detectOrganism,DataFrame-method	detectOrganism
detectOrganism,dgCMatrix-method	detectOrganism
detectOrganism,factor-method	detectOrganism
detectOrganism,matrix-method	detectOrganism
detectOrganism,tbl_df-method	detectOrganism
dots	dots
dotted	makeNames
dotted,ANY-method	makeNames
dotted,character-method	makeNames
dotted,data.frame-method	makeNames
dotted,DataFrame-method	makeNames
dotted,factor-method	makeNames
dotted,GRanges-method	makeNames
dotted,List-method	makeNames
dotted,list-method	makeNames
dotted,matrix-method	makeNames
dotted,SimpleList-method	makeNames
dynamicPlotlist	dynamicPlotlist
emptyRanges	emptyRanges
ensembl	deprecated
fc2lr	deprecated
fixNA	fixNA
fixNA,ANY-method	fixNA
fixNA,character-method	fixNA
fixNA,data.frame-method	fixNA
fixNA,DataFrame-method	fixNA
fixNA,tbl_df-method	fixNA
foldChangeToLogRatio	logRatio
foldChangeToLogRatio,integer-method	logRatio
foldChangeToLogRatio,numeric-method	logRatio
gene2symbolFromGFF	deprecated
gene2symbolFromGTF	deprecated
general	general
geomean	deprecated
geometricMean	geometricMean
geometricMean,data.frame-method	geometricMean
geometricMean,matrix-method	geometricMean
geometricMean,numeric-method	geometricMean
glimpse	reexports
grepString	grepString
hasRownames	assertHasRownames
hgnc2gene	hgnc2gene
initializeDir	deprecated
initializeDirectory	initializeDirectory
isAnImplicitInteger	assertIsImplicitInteger
isImplicitInteger	assertIsImplicitInteger
isURL	assertIsURL
is_tibble	reexports
kables	kables
loadData	loadData
loadDataAsName	loadDataAsName
loadRemoteData	loadRemoteData
localOrRemoteFile	localOrRemoteFile
logRatio	logRatio
logRatioToFoldChange	logRatio
logRatioToFoldChange,integer-method	logRatio
logRatioToFoldChange,numeric-method	logRatio
lr2fc	deprecated
makeGene2symbolFromEnsembl	makeGene2symbolFromEnsembl
makeGene2symbolFromGFF	makeGene2symbolFromGFF
makeGene2symbolFromGTF	makeGene2symbolFromGFF
makeGRangesFromEnsembl	makeGRangesFromEnsembl
makeGRangesFromGFF	makeGRangesFromGFF
makeGRangesFromGTF	makeGRangesFromGFF
makeNames	makeNames
makeTx2geneFromEnsembl	makeTx2geneFromEnsembl
makeTx2geneFromGFF	makeTx2geneFromGFF
makeTx2geneFromGTF	makeTx2geneFromGFF
markdownHeader	markdownHeader
markdownList	markdownList
markdownPlotlist	markdownPlotlist
Matrix	reexports
mcols	reexports
mdHeader	markdownHeader
mdList	markdownList
mdPlotlist	markdownPlotlist
metadataTable	deprecated
methodFormals	methodFormals
mgi2gene	mgi2gene
microplate	microplate
midnightTheme	themes
multiassignAsEnvir	multiassignAsEnvir
multiassignAsNewEnvir	deprecated
packageSE	deprecated
panther	panther
paperwhiteTheme	themes
parseGFFAttributes	parseGFFAttributes
pct	deprecated
prepareSE	deprecated
printString	printString
readFileByExtension	readFileByExtension
readGFF	readGFF
readGTF	readGFF
readJSON	readJSON
readYAML	readYAML
reexports	reexports
removeNA	removeNA
removeNA,ANY-method	removeNA
removeNA,atomic-method	removeNA
removeNA,data.frame-method	removeNA
removeNA,DataFrame-method	removeNA
removeNA,matrix-method	removeNA
revcomp	deprecated
rnaseqCounts	rnaseqCounts
sanitizeAnnotable	deprecated
sanitizeColData	deprecated
sanitizeRowData	sanitizeRowData
sanitizeSampleData	sanitizeSampleData
saveData	saveData
set_rownames	reexports
singleCellCounts	singleCellCounts
snake	makeNames
snake,ANY-method	makeNames
snake,character-method	makeNames
snake,data.frame-method	makeNames
snake,DataFrame-method	makeNames
snake,factor-method	makeNames
snake,GRanges-method	makeNames
snake,List-method	makeNames
snake,list-method	makeNames
snake,matrix-method	makeNames
snake,SimpleList-method	makeNames
sortUnique	sortUnique
stripTranscriptVersions	stripTranscriptVersions
stripTranscriptVersions,character-method	stripTranscriptVersions
stripTranscriptVersions,dgCMatrix-method	stripTranscriptVersions
stripTranscriptVersions,matrix-method	stripTranscriptVersions
summarizeRows	deprecated
symbol2gene	deprecated
synonyms	synonyms
themes	themes
theme_midnight	themes
theme_paperwhite	themes
tibble	reexports
toStringUnique	toStringUnique
transmit	transmit
tx2gene	deprecated
tx2geneFromGFF	deprecated
tx2geneFromGTF	deprecated
upperCamel	makeNames
upperCamel,ANY-method	makeNames
upperCamel,character-method	makeNames
upperCamel,data.frame-method	makeNames
upperCamel,DataFrame-method	makeNames
upperCamel,factor-method	makeNames
upperCamel,GRanges-method	makeNames
upperCamel,List-method	makeNames
upperCamel,list-method	makeNames
upperCamel,matrix-method	makeNames
upperCamel,SimpleList-method	makeNames
wash	deprecated
writeCounts	writeCounts
