API for acidgenomics/basejump
Base Functions for Bioinformatics

Global functions
%in%	Man page
Annotated-class	Man page
AsIs-class	Man page
AtomicList-class	Man page
CharacterList	Man page
CharacterList-class	Man page
DataFrame	Man page
DataFrame-class	Man page
DataFrameList	Man page
DataFrameList-class	Man page
Ensembl2Entrez	Man page
Ensembl2Entrez-class	Man page
EnsemblGenes-class	Man page
EnsemblTranscripts-class	Man page
Entrez2Ensembl	Man page
Entrez2Ensembl-class	Man page
EntrezGeneInfo	Man page
EntrezGeneInfo-class	Man page
Factor-class	Man page
FactorList	Man page
FactorList-class	Man page
FlyBaseGenes-class	Man page
FlyBaseTranscripts-class	Man page
GRanges	Man page
GRanges-class	Man page
GRangesList	Man page
GRangesList-class	Man page
GencodeGenes-class	Man page
GencodeTranscripts-class	Man page
Gene2Symbol	Man page
Gene2Symbol-class	Man page
HGNC	Man page
HGNC-class	Man page
HGNC2Ensembl	Man page
HGNC2Ensembl-class	Man page
IRanges	Man page
IRanges-class	Man page
IntegerList	Man page
IntegerList-class	Man page
LLint	Man page
LLint-class	Man page
List	Man page
List-class	Man page
LogicalList	Man page
LogicalList-class	Man page
MGI2Ensembl	Man page
MGI2Ensembl-class	Man page
Matrix	Man page
Matrix-class	Man page
NumericList	Man page
NumericList-class	Man page
Protein2Gene-class	Man page
RangedSummarizedExperiment-class	Man page
RectangularData-class	Man page
RefSeqGenes-class	Man page
RefSeqTranscripts-class	Man page
Rle	Man page
Rle-class	Man page
RleList	Man page
RleList-class	Man page
SimpleList	Man page
SimpleList-class	Man page
SingleCellExperiment	Man page
SingleCellExperiment-class	Man page
SplitDataFrameList	Man page
SplitDataFrameList-class	Man page
SummarizedExperiment	Man page
SummarizedExperiment-class	Man page
Tx2Gene	Man page
Tx2Gene-class	Man page
UCSCGenes-class	Man page
UCSCTranscripts-class	Man page
URLencode	Man page
Vector-class	Man page
WormBaseGenes-class	Man page
WormBaseTranscripts-class	Man page
aggregate	Man page
aggregateCellsToSamples	Man page
aggregateCols	Man page
aggregateRows	Man page
alert	Man page
alertDanger	Man page
alertInfo	Man page
alertSuccess	Man page
alertWarning	Man page
annotable	Man page
antiJoin	Man page
anyDuplicated	Man page
append	Man page
appendToBody	Man page
arrow	Man page
as	Man page
as.DataFrame	Man page
as.SummarizedExperiment	Man page
as.data.frame	Man page
as.data.table	Man page
as.factor	Man page
as.formula	Man page
as.list	Man page
as.matrix	Man page
as.table	Man page
as.vector	Man page
as_tibble	Man page
assay	Man page
assay<-	Man page
assayNames	Man page
assayNames<-	Man page
assays	Man page
assays<-	Man page
assignAndSaveData	Man page
atomic-class	Man page
atomize	Man page
autopadZeros	Man page
axisTicks	Man page
barcodePattern	Man page
basejump	Man page
basejump-package	Man page
basejumpTestsURL	Man page Source code
basename	Man page
basenameSansExt	Man page
cacheURL	Man page
calculateMetrics	Man page
camelCase	Man page
capitalize	Man page
capture.output	Man page
cbind	Man page
cell2sample	Man page
classContains	Man page
coerce	Man page
coerceToList	Man page
colData	Man page
colData<-	Man page
colSums	Man page
collapseToString	Man page
colnames	Man page
colnames<-	Man page
colorRampPalette	Man page
column_to_rownames	Man page
combine	Man page
complete.cases	Man page
compress	Man page
compressExtPattern	Man page
convertGenesToSymbols	Man page
convertSampleIDsToNames	Man page
convertSymbolsToGenes	Man page
convertTranscriptsToGenes	Man page
cor	Man page
correlation	Man page
counts	Man page
counts<-	Man page
currentEnsemblGenomeBuild	Man page
currentEnsemblVersion	Man page
currentFlyBaseVersion	Man page
currentGencodeGenomeBuild	Man page
currentGencodeVersion	Man page
currentRefSeqGenomeBuild	Man page
currentRefSeqVersion	Man page
currentUCSCGenomeBuild	Man page
currentWormBaseVersion	Man page
data	Man page
decode	Man page
decompress	Man page
defunct	Man page
deprecated	Man page
detectLanes	Man page
detectOrganism	Man page
dims	Man page
dirname	Man page
dist	Man page
dl	Man page
do.call	Man page
dots	Man page
dottedCase	Man page
download	Man page
downloadEnsemblGenome	Man page
downloadGencodeGenome	Man page
downloadRefSeqGenome	Man page
downloadUCSCGenome	Man page
droplevels	Man page
duplicated	Man page
ecdf	Man page
emptyRanges	Man page
encode	Man page
end	Man page
end<-	Man page
estimateSizeFactors	Man page
eval	Man page
expand	Man page
expand.grid	Man page
export	Man page
extPattern	Man page
factorize	Man page
fileDepth	Man page
fileExt	Man page
filterCells	Man page
foldChangeToLogRatio	Man page
forceDetach	Man page
formalArgs	Man page
formalsList	Man page
formula	Man page
fullJoin	Man page
geneNames	Man page
geneSynonyms	Man page
genomeMetadataNames	Man page
geometricMean	Man page
get	Man page
getListElement	Man page
getS3method	Man page
getURL	Man page
getURLDirList	Man page
grep	Man page
grepl	Man page
gsub	Man page
h1	Man page
h2	Man page
h3	Man page
h4	Man page
h5	Man page
h6	Man page
h7	Man page
hclust	Man page
head	Man page
headtail	Man page
humanize	Man page
import	Man page
importSampleData	Man page
importTx2Gene	Man page
initDir	Man page
innerJoin	Man page
integerCounts	Man page
interestingGroups	Man page
interestingGroups<-	Man page
intersect	Man page
intersectAll	Man page
intersectionMatrix	Man page
is	Man page
is.unsorted	Man page
kebabCase	Man page
lanePattern	Man page
lapply	Man page
leftJoin	Man page
loadData	Man page
loadDataAsName	Man page
loadRemoteData	Man page
localOrRemoteFile	Man page
logRatioToFoldChange	Man page
logcounts	Man page
logcounts<-	Man page
majorVersion	Man page
makeDimnames	Man page
makeGRangesFromEnsDb	Man page
makeGRangesFromEnsembl	Man page
makeGRangesFromGFF	Man page
makeGene2SymbolFromEnsDb	Man page
makeGene2SymbolFromEnsembl	Man page
makeGene2SymbolFromGFF	Man page
makeLabel	Man page
makeNames	Man page
makeProtein2GeneFromEnsembl	Man page
makeSampleData	Man page
makeSingleCellExperiment	Man page
makeSummarizedExperiment	Man page
makeTitle	Man page
makeTx2GeneFromEnsDb	Man page
makeTx2GeneFromEnsembl	Man page
makeTx2GeneFromFASTA	Man page
makeTx2GeneFromGFF	Man page
makeWords	Man page
mapCellsToSamples	Man page
mapEnsemblBuildToUCSC	Man page
mapEnsemblReleaseToURL	Man page
mapGenesToIDs	Man page
mapGenesToRownames	Man page
mapGenesToSymbols	Man page
mapHumanOrthologs	Man page
mapToDataFrame	Man page
mapUCSCBuildToEnsembl	Man page
mapply	Man page
markdownHeader	Man page
markdownLink	Man page
markdownList	Man page
markdownPlots	Man page
markdownTables	Man page
match	Man page
matchArgsToDoCall	Man page Source code
matchEnsemblReleaseToURL	Man page Source code
matchHumanOrthologs	Man page Source code
matchInterestingGroups	Man page
matchSampleColumn	Man page
matchesGene2Symbol	Man page
matchesInterestingGroups	Man page
mcols	Man page
mcols<-	Man page
mdHeader	Man page
mdLink	Man page
mdList	Man page
mdPlots	Man page
mdTables	Man page
mean	Man page
median	Man page
melt	Man page
merge	Man page
metadata	Man page
metadata2	Man page
metadata2<-	Man page
metadata<-	Man page
metadataBlacklist	Man page
metadataDenylist	Man page
methodFormals	Man page
methodFunction	Man page
metrics	Man page
metricsCols	Man page
metricsPerSample	Man page
mget	Man page
microplate	Man page
minimalSampleData	Man page
minorVersion	Man page
missingOrNULL-class	Man page
model.matrix	Man page
multiassignAsEnvir	Man page Source code
mutateAll	Man page
mutateAt	Man page
mutateIf	Man page
na.omit	Man page
naStrings	Man page
ncol	Man page
new	Man page
nonzeroRowsAndCols	Man page
normcounts	Man page
normcounts<-	Man page
nrow	Man page
ol	Man page
order	Man page
organism	Man page
organism<-	Man page
packageName	Man page
packageVersion	Man page
paste	Man page
pasteURL	Man page
pmax	Man page
pmax.int	Man page
pmin	Man page
pmin.int	Man page
pos	Man page
prcomp	Man page
prepareTemplate	Man page
printString	Man page
quantile	Man page
ranges	Man page
rank	Man page
rankedMatrix	Man page
rbind	Man page
rbindToDataFrame	Man page
rbindlist	Man page
readSampleData	Man page Source code
readTx2Gene	Man page Source code
realpath	Man page
reducedDim	Man page
reducedDim<-	Man page
reducedDimNames	Man page
reducedDimNames<-	Man page
reducedDims	Man page
reducedDims<-	Man page
reexports	Man page
relevel	Man page
relist	Man page
removeNA	Man page
reorder	Man page
rep.int	Man page
requireNamespaces	Man page
rgb	Man page
rightJoin	Man page
rowData	Man page
rowData<-	Man page
rowMeans	Man page
rowRanges	Man page
rowRanges<-	Man page
rowSums	Man page
rownames	Man page
rownames<-	Man page
rownames_to_column	Man page
sampleData	Man page
sampleData<-	Man page
sampleNames	Man page
sampleNames<-	Man page
sanitizeNA	Man page
sanitizePercent	Man page
sanitizeSampleData	Man page
sanitizeVersion	Man page
sapply	Man page
saveData	Man page
sd	Man page
selectIf	Man page
selectSamples	Man page
sem	Man page
semiJoin	Man page
sentenceCase	Man page
separator	Man page
seqnames	Man page
sessionInfo	Man page
session_info	Man page
setdiff	Man page
shell	Man page
showHeader	Man page
showSlotInfo	Man page
sizeFactors	Man page
sizeFactors<-	Man page
snakeCase	Man page
sort	Man page
sortUnique	Man page Source code
sparseMatrix	Man page
sparseMatrix-class	Man page
split	Man page
splitByLevel	Man page
standardizeCall	Man page
start	Man page
start<-	Man page
str_detect	Man page
str_dup	Man page
str_extract	Man page
str_extract_all	Man page
str_length	Man page
str_locate_all	Man page
str_match	Man page
str_match_all	Man page
str_pad	Man page
str_replace	Man page
str_replace_all	Man page
str_replace_na	Man page
str_split	Man page
str_split_fixed	Man page
str_sub	Man page
str_subset	Man page
str_trunc	Man page
stripGeneVersions	Man page
stripTranscriptVersions	Man page
sub	Man page
subset	Man page
subsetPerSample	Man page
summary	Man page
t	Man page
table	Man page
tail	Man page
tapply	Man page
tibble	Man page
toInlineString	Man page
toStringUnique	Man page Source code
topCellsPerSample	Man page
tpm	Man page
transmit	Man page
transmuteAt	Man page
transmuteIf	Man page
trim	Man page
txt	Man page
ul	Man page
union	Man page
unique	Man page
unit	Man page
uniteInterestingGroups	Man page
unlist	Man page
unlistToDataFrame	Man page
unsplit	Man page
untar	Man page
updateMessage	Man page
upperCamelCase	Man page
validObject	Man page
var	Man page
verbatim	Man page
which	Man page
which.max	Man page
which.min	Man page
width	Man page
width<-	Man page
zerosVsDepth	Man page