Man pages for acidgenomics/basejump
Base Functions for Bioinformatics

aggregateAggregate rows or columns
aggregateCellsToSamplesAggregate cells to samples
alphaThresholdAlpha threshold
autopadZerosAutopad zeros
barcodePatternSingle-sell barcode pattern
basejump-packagebasejump
basejumpTestsURLbasejump test data URL
calculateMetricsCalculate quality control metrics
camelCaseCamel case
cell2sampleCell-to-sample mappings
collapseToStringCollapse to string
combineCombining or merging different Bioconductor data structures
convertGenesToSymbolsConvert genes to symbols
convertSampleIDsToNamesConvert sample identifiers to names
convertTranscriptsToGenesConvert transcripts to genes
correlationCorrelation
countsCounts
defunctDefunct functions
deprecatedDeprecated functions
detectHPCDetect HPC environment
detectLanesDetect sequencing lanes
dottedCaseDotted case
Ensembl2EntrezEnsembl-to-Entrez gene identifier mappings
Ensembl2Entrez-classEnsembl-to-Entrez gene identifier mappings
estimateSizeFactorsEstimate size factors
filterCellsFilter cells
formalsListShared list of optional default formals
Gene2SymbolGene-to-symbol mappings
Gene2Symbol-classGene-to-symbol mappings
geneNamesGene names
geneSynonymsGene synonyms
genomeMetadataNamesSlot names in metadata containing genome information
genomeVersionsGenome versions
geometricMeanGeometric mean
headtailReturn the first and last parts of an object
HGNC2EnsemblHGNC-to-Ensembl gene identifier mappings
HGNC2Ensembl-classHGNC-to-Ensembl gene identifier mappings
humanizeHumanize an R object
importSampleDataImport sample metadata
importTx2GeneImport transcript-to-gene annotations
interestingGroupsInteresting groups
lanePatternSequencing lane grep pattern
lfcThresholdLog2 fold change threshold
logRatioInterconvert log ratio and fold change values
makeGene2SymbolMake a Gene2Symbol object
makeSampleDataMake sample data
makeSingleCellExperimentMake a SingleCellExperiment object
makeSummarizedExperimentMake a SummarizedExperiment object
makeTx2GeneMake a Tx2Gene object
makeTx2GeneFromFASTAMake a Tx2Gene object from transcriptome FASTA
mapCellsToSamplesMap cells to samples
mapGenesMap genes
markdownMarkdown
markdownHeaderMarkdown header
markdownLinkMarkdown hyperlink
markdownListMarkdown list
markdownPlotsMultiple Markdown plots
markdownTablesMultiple Markdown tables
matchEnsemblReleaseToURLMatch Ensembl release to archive URL.
matchesGene2SymbolCheck that user-defined gene input matches expected values
matchesInterestingGroupsCheck that interesting groups match a defined value
matchHumanOrthologsMatch human gene orthologs
matchInterestingGroupsMatch interesting groups
mcolnamesMetadata column names
meltMelt columns into key-value pairs
metadataBlacklistSample metadata blacklist
metricsQuality control metrics
metricsColsQuality control metric columns
MGI2EnsemblMGI-to-Ensembl gene identifier mappings
MGI2Ensembl-classMGI-to-Ensembl gene identifier mappings
microplateMicrotiter plate well identifiers
minimalSampleDataMinimal sample data
multiassignAsEnvirAssign multiple objects into a new environment
nonzeroRowsAndColsSubset object to keep only non-zero rows and columns
organismOrganism
prepareTemplatePrepare R Markdown template
pseudobulkPseudobulk
rankedMatrixCalculate a ranked matrix
reexportsObjects exported from other packages
sampleDataSample data
sampleNamesSample names
sanitizeSampleDataSanitize sample data
selectSamplesSelect samples
separatorSeparator bar
showHeaderHeader for object show method
showSlotInfoShow slot information
sizeFactorsSize factors
snakeCaseSnake case
sortUniqueSort and make unique
stripTranscriptVersionsStrip transcript versions
subsetPerSampleSubset per sample
summaryObject summaries
topCellsPerSampleTop cells per sample
toStringUniqueConvert to a unique character string
tpmTranscripts per million
Tx2GeneTranscript-to-gene identifier mappings
Tx2Gene-classTranscript-to-gene identifier mappings
uniteInterestingGroupsUnite interesting groups into a single column
updateMessageUpdate message
upperCamelCaseUpper camel case
zerosVsDepthPercentage of zeros vs. library depth
acidgenomics/basejump documentation built on Nov. 12, 2019, 8:49 a.m.