API for acidgenomics/basejump
Base Functions for Bioinformatics

Global functions
%$% Man page
%<>% Man page
%>% Man page
%T>% Man page
.aggregateMessage Source code
.centerSizeFactors Source code
.isSampleData Source code
.mapGenes Source code
.melt Source code
.slotGenomeMetadata Source code
DataFrame Man page
Ensembl2Entrez Man page
Ensembl2Entrez,DataFrame-method Man page
Ensembl2Entrez,GRanges-method Man page
Ensembl2Entrez,SummarizedExperiment-method Man page
Ensembl2Entrez-class Man page
GRanges Man page
GRangesList Man page
Gene2Symbol Man page
Gene2Symbol,DataFrame-method Man page
Gene2Symbol,GRanges-method Man page
Gene2Symbol,SummarizedExperiment-method Man page
Gene2Symbol-class Man page
HGNC2Ensembl Man page
HGNC2Ensembl-class Man page
IRanges Man page
MGI2Ensembl Man page Source code
MGI2Ensembl-class Man page
SimpleList Man page
Tx2Gene Man page
Tx2Gene,DataFrame-method Man page
Tx2Gene,GRanges-method Man page
Tx2Gene,SummarizedExperiment-method Man page
Tx2Gene,data.frame-method Man page
Tx2Gene,matrix-method Man page
Tx2Gene-class Man page
`makeSingleCellExperiment,SimpleList` Source code
`makeSummarizedExperiment,SimpleList` Source code
aggregate Man page
aggregateCellsToSamples Man page
aggregateCellsToSamples,SingleCellExperiment-method Man page
aggregateCols Man page
aggregateCols,SingleCellExperiment-method Man page
aggregateCols,SummarizedExperiment-method Man page
aggregateCols,matrix-method Man page
aggregateCols,sparseMatrix-method Man page
aggregateRows Man page
aggregateRows,SummarizedExperiment-method Man page
aggregateRows,matrix-method Man page
aggregateRows,sparseMatrix-method Man page
alphaThreshold Man page
alphaThreshold,Annotated-method Man page
alphaThreshold<- Man page
alphaThreshold<-,Annotated,numeric-method Man page
annotable Man page
antiJoin Man page
as.SummarizedExperiment Man page
as.data.frame Man page
as.data.table Man page
as_tibble Man page
assay Man page
assay<- Man page
assayNames Man page
assays Man page
assays<- Man page
assignAndSaveData Man page
atomize Man page
autopadZeros Man page
autopadZeros,SummarizedExperiment-method Man page
autopadZeros,character-method Man page
autopadZeros,matrix-method Man page
barcodePattern Man page
basejump Man page
basejump-package Man page
basejumpTestsURL Man page
basenameSansExt Man page
bunzip2 Man page
bzip2 Man page
calculateMetrics Man page
calculateMetrics,Matrix-method Man page
calculateMetrics,RangedSummarizedExperiment-method Man page
calculateMetrics,SingleCellExperiment-method Man page
calculateMetrics,matrix-method Man page
camel Man page
camelCase Man page
camelCase,DataTable-method Man page
camelCase,Matrix-method Man page
camelCase,Ranges-method Man page
camelCase,SummarizedExperiment-method Man page
camelCase,Vector-method Man page
camelCase,atomic-method Man page
camelCase,data.frame-method Man page
camelCase,factor-method Man page
camelCase,list-method Man page
camelCase,matrix-method Man page
capitalize Man page
cell2sample Man page
cell2sample,SingleCellExperiment-method Man page
coerceS4ToList Man page
colData Man page
colData<- Man page
collapseToString Man page
collapseToString,DataFrame-method Man page
collapseToString,atomic-method Man page
collapseToString,data.frame-method Man page
collapseToString,matrix-method Man page
combine Man page
combine,SingleCellExperiment,SingleCellExperiment-method Man page
combine,SummarizedExperiment,SummarizedExperiment-method Man page
compressFile Man page
convertGenesToSymbols Man page
convertGenesToSymbols,SummarizedExperiment-method Man page
convertGenesToSymbols,character-method Man page
convertGenesToSymbols,matrix-method Man page
convertGenesToSymbols,sparseMatrix-method Man page
convertSampleIDsToNames Man page
convertSampleIDsToNames,SingleCellExperiment-method Man page
convertSampleIDsToNames,SummarizedExperiment-method Man page
convertSymbolsToGenes Man page
convertSymbolsToGenes,SummarizedExperiment-method Man page
convertTranscriptsToGenes Man page
convertTranscriptsToGenes,SummarizedExperiment-method Man page
convertTranscriptsToGenes,character-method Man page
convertTranscriptsToGenes,matrix-method Man page
convertTranscriptsToGenes,sparseMatrix-method Man page
convertUCSCBuildToEnsembl Man page
correlation Man page
correlation,Matrix,Matrix-method Man page
correlation,Matrix,missingOrNULL-method Man page
correlation,SummarizedExperiment,SummarizedExperiment-method Man page
correlation,SummarizedExperiment,missingOrNULL-method Man page
correlation,matrix,matrix-method Man page
correlation,matrix,missingOrNULL-method Man page
correlation,numeric,numeric-method Man page
counts Man page
counts,SummarizedExperiment-method Man page
counts<- Man page
counts<-,SummarizedExperiment,Matrix-method Man page
counts<-,SummarizedExperiment,matrix-method Man page
decode Man page
decompressFile Man page
defunct Man page
deprecated Man page
detectHPC Man page Source code
detectLanes Man page Source code
detectOrganism Man page
dots Man page
dotted Man page
dottedCase Man page
dottedCase,DataTable-method Man page
dottedCase,Matrix-method Man page
dottedCase,Ranges-method Man page
dottedCase,SummarizedExperiment-method Man page
dottedCase,Vector-method Man page
dottedCase,atomic-method Man page
dottedCase,data.frame-method Man page
dottedCase,factor-method Man page
dottedCase,list-method Man page
dottedCase,matrix-method Man page
emptyRanges Man page
encode Man page
ensemblVersion Man page Source code
estimateSizeFactors Man page
estimateSizeFactors,SingleCellExperiment-method Man page
estimateSizeFactors,SummarizedExperiment-method Man page
export Man page
factorize Man page
fileExt Man page
filterCells Man page
filterCells,SingleCellExperiment-method Man page
flatFiles Man page
flybaseVersion Man page Source code
foldChangeToLogRatio Man page
foldChangeToLogRatio,numeric-method Man page
formalsList Man page
fullJoin Man page
gencodeVersion Man page Source code
geneNames Man page
geneNames,GRanges-method Man page
geneNames,SummarizedExperiment-method Man page
geneSynonyms Man page Source code
genomeMetadataNames Man page
genomeVersions Man page
geometricMean Man page
geometricMean,matrix-method Man page
geometricMean,numeric-method Man page
geometricMean,sparseMatrix-method Man page
getURL Man page
getURLDirList Man page
gunzip Man page
gzip Man page
headtail Man page
headtail,DataFrame-method Man page
headtail,GRanges-method Man page
headtail,SummarizedExperiment-method Man page
headtail,atomic-method Man page
headtail,data.frame-method Man page
headtail,matrix-method Man page
headtail,sparseMatrix-method Man page
humanize Man page
humanize,SummarizedExperiment-method Man page
import Man page
importSampleData Man page Source code
importTx2Gene Man page Source code
initDir Man page
innerJoin Man page
interestingGroups Man page
interestingGroups,Annotated-method Man page
interestingGroups<- Man page
interestingGroups<-,Annotated,NULL-method Man page
interestingGroups<-,Annotated,character-method Man page
interestingGroups<-,SummarizedExperiment,character-method Man page
kebab Man page
kebabCase Man page
lanePattern Man page
leftJoin Man page
lfcThreshold Man page
lfcThreshold,Annotated-method Man page
lfcThreshold<- Man page
lfcThreshold<-,Annotated,numeric-method Man page
loadData Man page
loadDataAsName Man page
loadRemoteData Man page
localOrRemoteFile Man page
logRatio Man page
logRatioToFoldChange Man page
logRatioToFoldChange,numeric-method Man page
makeDimnames Man page
makeGRangesFromEnsDb Man page
makeGRangesFromEnsembl Man page
makeGRangesFromGFF Man page
makeGRangesFromGTF Man page
makeGene2Symbol Man page
makeGene2SymbolFromEnsDb Man page Source code
makeGene2SymbolFromEnsembl Man page Source code
makeGene2SymbolFromGFF Man page Source code
makeGene2SymbolFromGTF Man page
makeLabel Man page
makeNames Man page
makeSampleData Man page
makeSampleData,DataFrame-method Man page
makeSampleData,data.frame-method Man page
makeSingleCellExperiment Man page
makeSingleCellExperiment,SimpleList-method Man page
makeSingleCellExperiment,list-method Man page
makeSummarizedExperiment Man page
makeSummarizedExperiment,SimpleList-method Man page
makeSummarizedExperiment,list-method Man page
makeTitle Man page
makeTx2Gene Man page
makeTx2GeneFromEnsDb Man page Source code
makeTx2GeneFromEnsembl Man page Source code
makeTx2GeneFromFASTA Man page Source code
makeTx2GeneFromGFF Man page Source code
makeTx2GeneFromGTF Man page
makeWords Man page
mapCellsToSamples Man page Source code
mapGenes Man page
mapGenesToIDs Man page
mapGenesToIDs,Gene2Symbol-method Man page
mapGenesToIDs,SummarizedExperiment-method Man page
mapGenesToRownames Man page
mapGenesToRownames,Gene2Symbol-method Man page
mapGenesToRownames,SummarizedExperiment-method Man page
mapGenesToSymbols Man page
mapGenesToSymbols,Gene2Symbol-method Man page
mapGenesToSymbols,SummarizedExperiment-method Man page
markdown Man page
markdown,SummarizedExperiment-method Man page
markdownHeader Man page Source code
markdownLink Man page Source code
markdownList Man page Source code
markdownPlots Man page Source code
markdownTables Man page Source code
matchArgsToDoCall Man page
matchEnsemblReleaseToURL Man page Source code
matchHumanOrthologs Man page Source code
matchInterestingGroups Man page Source code
matchesGene2Symbol Man page Source code
matchesInterestingGroups Man page Source code
mcolnames Man page
mcolnames,Vector-method Man page
mcolnames<- Man page
mcolnames<-,Vector,character-method Man page
mcols Man page
mcols<- Man page
mdHeader Man page
mdLink Man page
mdList Man page
mdPlots Man page
mdTables Man page
melt Man page
melt,DataFrame-method Man page
melt,Matrix-method Man page
melt,SingleCellExperiment-method Man page
melt,SummarizedExperiment-method Man page
melt,matrix-method Man page
melt,table-method Man page
metadata Man page
metadata2 Man page
metadata2<- Man page
metadata<- Man page
metadataBlacklist Man page
methodFormals Man page
methodFunction Man page
metrics Man page
metrics,SingleCellExperiment-method Man page
metrics,SummarizedExperiment-method Man page
metricsCols Man page
metricsPerSample Man page
metricsPerSample,SingleCellExperiment-method Man page
microplate Man page Source code
minimalSampleData Man page Source code
multiassignAsEnvir Man page Source code
mutateAll Man page
mutateAt Man page
mutateIf Man page
naStrings Man page
nonzeroRowsAndCols Man page
nonzeroRowsAndCols,Matrix-method Man page
nonzeroRowsAndCols,SummarizedExperiment-method Man page
nonzeroRowsAndCols,matrix-method Man page
organism Man page
organism,Annotated-method Man page
organism,DataTable-method Man page
organism,GRanges-method Man page
organism,SummarizedExperiment-method Man page
organism,data.frame-method Man page
organism,matrix-method Man page
organism,sparseMatrix-method Man page
organism<- Man page
organism<-,Annotated-method Man page
pasteURL Man page
plotGene Man page
prepareTemplate Man page Source code
printString Man page
pseudobulk Man page
pseudobulk,SingleCellExperiment-method Man page
rankedMatrix Man page Source code
readFileByExtension Man page Source code
readGFF Man page Source code
readGTF Man page Source code
readJSON Man page Source code
readSampleData Man page Source code
readTx2Gene Man page Source code
readYAML Man page Source code
realpath Man page
reducedDims Man page
reducedDims<- Man page
reexports Man page
refseqVersion Man page Source code
relevel Man page
relevelColData Man page Source code
relevelRowData Man page Source code
relevelRowRanges Man page Source code
removeNA Man page
rightJoin Man page
rowData Man page
rowData<- Man page
rowRanges Man page
rowRanges<- Man page
sampleData Man page
sampleData,SingleCellExperiment-method Man page
sampleData,SummarizedExperiment-method Man page
sampleData<- Man page
sampleData<-,SingleCellExperiment,DataFrame-method Man page
sampleData<-,SummarizedExperiment,DataFrame-method Man page
sampleNames Man page
sampleNames,SummarizedExperiment-method Man page
sampleNames<- Man page
sampleNames<-,SummarizedExperiment,character-method Man page
sanitizeNA Man page
sanitizePercent Man page
sanitizeSampleData Man page Source code
saveData Man page
selectIf Man page
selectSamples Man page
selectSamples,SingleCellExperiment-method Man page
selectSamples,SummarizedExperiment-method Man page
semiJoin Man page
separator Man page Source code
separatorBar Man page Source code
showHeader Man page Source code
showSlotInfo Man page Source code
sizeFactors Man page
sizeFactors,SummarizedExperiment-method Man page
sizeFactors<- Man page
sizeFactors<-,SummarizedExperiment-method Man page
snake Man page
snakeCase Man page
snakeCase,DataTable-method Man page
snakeCase,Matrix-method Man page
snakeCase,Ranges-method Man page
snakeCase,SummarizedExperiment-method Man page
snakeCase,Vector-method Man page
snakeCase,atomic-method Man page
snakeCase,data.frame-method Man page
snakeCase,factor-method Man page
snakeCase,list-method Man page
snakeCase,matrix-method Man page
sortUnique Man page Source code
standardizeCall Man page
stripGeneVersions Man page Source code
stripTranscriptVersions Man page
stripTranscriptVersions,SummarizedExperiment-method Man page
stripTranscriptVersions,character-method Man page
stripTranscriptVersions,matrix-method Man page
stripTranscriptVersions,sparseMatrix-method Man page
subsetPerSample Man page
subsetPerSample,SingleCellExperiment-method Man page
summary Man page
summary,Gene2Symbol-method Man page
summary,Tx2Gene-method Man page
tar Man page
theme_midnight Man page Source code
theme_paperwhite Man page Source code
tibble Man page
toStringUnique Man page Source code
topCellsPerSample Man page
topCellsPerSample,SingleCellExperiment-method Man page
tpm Man page
tpm,SummarizedExperiment-method Man page
transmit Man page
transmuteAt Man page
transmuteIf Man page
tx2geneFromGFF Man page Source code
uniteInterestingGroups Man page
uniteInterestingGroups,DataFrame-method Man page
uniteInterestingGroups,data.frame-method Man page
untar Man page
unzip Man page
updateMessage Man page
upperCamel Man page
upperCamelCase Man page
upperCamelCase,DataTable-method Man page
upperCamelCase,Matrix-method Man page
upperCamelCase,Ranges-method Man page
upperCamelCase,SummarizedExperiment-method Man page
upperCamelCase,Vector-method Man page
upperCamelCase,atomic-method Man page
upperCamelCase,data.frame-method Man page
upperCamelCase,factor-method Man page
upperCamelCase,list-method Man page
upperCamelCase,matrix-method Man page
wormbaseVersion Man page Source code
writeCounts Man page
zerosVsDepth Man page
zerosVsDepth,SingleCellExperiment-method Man page
zerosVsDepth,SummarizedExperiment-method Man page
zerosVsDepth,matrix-method Man page
zerosVsDepth,sparseMatrix-method Man page
zip Man page
acidgenomics/basejump documentation built on Nov. 12, 2019, 8:49 a.m.