These objects are imported from other packages. Follow the links below to see their documentation.

AcidBase

URLencode, addToPathEnd, addToPathStart, appendToBody, arrow, as.formula, axisTicks, barcodePattern, basenameSansExt, capture.output, classContains, collapseToPathString, colorRampPalette, compress, compressExtPattern, data, decompress, dist, dots, download, ecdf, extPattern, fileDepth, fileExt, forceDetach, formalsList, formula, genomeMetadataNames, getS3method, hclust, initDir, lanePattern, majorVersion, metadataDenylist, methodFormals, methodFunction, metricsCols, minorVersion, model.matrix, packageName, packageVersion, parentDir, parentDirectory, pasteURL, prcomp, printString, realpath, relevel, removeFromPath, reorder, requireNamespaces, rgb, sanitizeVersion, sessionInfo, shell, showSlotInfo, simpleClass, splitPathString, standardizeCall, tar, uniquePathString, unit, untar, updateMessage

AcidCLI

abort, alert, alertDanger, alertInfo, alertSuccess, alertWarning, dl, h1, h2, h3, h4, h5, h6, h7, inform, ol, separator, toInlineString, txt, ul, verbatim, warn

AcidExperiment

SummarizedExperiment, assay, assay<-, assayNames, assayNames<-, assays, assays<-, colData, colData<-, detectLanes, importSampleData, makeSummarizedExperiment, matchInterestingGroups, microplate, minimalSampleData, rowData, rowData<-, rowRanges, rowRanges<-, sanitizeSampleData, session_info

AcidGenerics

%in%, CharacterList, DataFrame, DataFrameList, FactorList, IRanges, IntegerList, LLint, List, LogicalList, NumericList, Rle, RleList, SimpleList, SplitDataFrameList, aggregate, aggregateCellsToSamples, aggregateCols, aggregateRows, antiJoin, anyDuplicated, append, as.DataFrame, as.SummarizedExperiment, as.data.frame, as.factor, as.list, as.matrix, as.table, as.vector, atomize, autopadZeros, basename, calculateMetrics, camelCase, capitalize, cbind, cell2sample, coerce, coerceToList, colSums, collapseToString, colnames, colnames<-, combine, complete.cases, convertGenesToSymbols, convertSampleIDsToNames, convertSymbolsToGenes, convertTranscriptsToGenes, cor, correlation, counts, counts<-, decode, dims, dirname, do.call, dottedCase, droplevels, duplicated, encode, end, end<-, estimateSizeFactors, eval, expand, expand.grid, export, factorize, filterCells, foldChangeToLogRatio, fullJoin, geneNames, geometricMean, get, getListElement, grep, grepl, gsub, head, headtail, humanize, innerJoin, integerCounts, interestingGroups, interestingGroups<-, intersect, intersectAll, intersectionMatrix, is.unsorted, kebabCase, lapply, leftJoin, logRatioToFoldChange, makeDimnames, makeLabel, makeNames, makeSampleData, makeTitle, makeWords, mapGenesToIDs, mapGenesToRownames, mapGenesToSymbols, mapToDataFrame, mapply, match, matchSampleColumn, mcols, mcols<-, mean, median, melt, merge, metadata, metadata2, metadata2<-, metadata<-, metrics, metricsPerSample, mget, mutateAll, mutateAt, mutateIf, na.omit, ncol, nonzeroRowsAndCols, nrow, order, organism, organism<-, paste, pmax, pmax.int, pmin, pmin.int, pos, quantile, ranges, rank, rankedMatrix, rbind, rbindToDataFrame, relist, removeNA, rep.int, rightJoin, rowMeans, rowSums, rownames, rownames<-, sampleData, sampleData<-, sampleNames, sampleNames<-, sanitizeNA, sanitizePercent, sapply, sd, selectIf, selectSamples, sem, semiJoin, sentenceCase, setdiff, setdiff, showHeader, sizeFactors, sizeFactors<-, snakeCase, sort, split, splitByLevel, start, start<-, stripGeneVersions, stripTranscriptVersions, sub, subset, subsetPerSample, summary, t, table, tail, tapply, topCellsPerSample, tpm, transmuteAt, transmuteIf, trim, union, unique, uniteInterestingGroups, unlist, unsplit, upperCamelCase, var, which, which.max, which.min, width, width<-, zerosVsDepth

AcidGenomes

Ensembl2Entrez, Entrez2Ensembl, EntrezGeneInfo, Gene2Symbol, HGNC, HGNC2Ensembl, MGI2Ensembl, Tx2Gene, annotable, currentEnsemblGenomeBuild, currentEnsemblVersion, currentFlyBaseVersion, currentGencodeGenomeBuild, currentGencodeVersion, currentRefSeqGenomeBuild, currentRefSeqVersion, currentUCSCGenomeBuild, currentWormBaseVersion, detectOrganism, downloadEnsemblGenome, downloadGencodeGenome, downloadRefSeqGenome, downloadUCSCGenome, emptyRanges, geneSynonyms, importTx2Gene, makeGRangesFromEnsDb, makeGRangesFromEnsembl, makeGRangesFromGFF, makeGene2SymbolFromEnsDb, makeGene2SymbolFromEnsembl, makeGene2SymbolFromGFF, makeProtein2GeneFromEnsembl, makeTx2GeneFromEnsDb, makeTx2GeneFromEnsembl, makeTx2GeneFromFASTA, makeTx2GeneFromGFF, mapEnsemblReleaseToURL, mapHumanOrthologs

AcidMarkdown

markdownHeader, markdownLink, markdownList, markdownPlots, markdownTables, mdHeader, mdLink, mdList, mdPlots, mdTables, prepareTemplate

AcidSingleCell

SingleCellExperiment, logcounts, logcounts<-, makeSingleCellExperiment, mapCellsToSamples, normcounts, normcounts<-, reducedDim, reducedDim<-, reducedDimNames, reducedDimNames<-, reducedDims, reducedDims<-

pipette

GRanges, GRangesList, Matrix, as.data.table, as_tibble, assignAndSaveData, cacheURL, column_to_rownames, getURL, getURLDirList, import, loadData, loadDataAsName, loadRemoteData, localOrRemoteFile, naStrings, rbindlist, rownames_to_column, saveData, seqnames, sparseMatrix, tibble, transmit

stringr

str_detect, str_dup, str_extract, str_extract_all, str_length, str_locate_all, str_match, str_match_all, str_pad, str_replace, str_replace_all, str_replace_na, str_split, str_split_fixed, str_sub, str_subset, str_trunc

syntactic

syntacticRename