Files in acidgenomics/AcidGenerics

Acid Genomics Generics

NEWS.md R/EnsemblToNcbi.R R/GeneToSymbol.R R/KnownMarkers.R R/NcbiToEnsembl.R R/TxToGene.R R/aggregateCellsToSamples.R R/aggregateCols.R R/aggregateRows.R R/alphaSummary.R R/alphaThreshold.R R/as.DESeqDataSet.R R/as.DESeqTransform.R R/as.DGEList.R R/as.DataFrame.R R/as.Seurat.R R/as.SingleCellExperiment.R R/as.SummarizedExperiment.R R/atomize.R R/autopadZeros.R R/barcodeRanksPerSample.R R/baseMeanThreshold.R R/calculateMetrics.R R/camelCase.R R/capitalize.R R/cast.R R/cellCountsPerCluster.R R/cellToSample.R R/cellTypesPerCluster.R R/cellsPerGeneFusion.R R/cellsPerMutation.R R/clusters.R R/coerceToList.R R/collapseToString.R R/collectionNames.R R/contrastName.R R/contrastNames.R R/contrastSamples.R R/convertGenesToSymbols.R R/convertSampleIdsToNames.R R/convertSymbolsToGenes.R R/convertToHuman.R R/convertTranscriptsToGenes.R R/correlation.R R/cpm.R R/deg.R R/degIntersection.R R/degPerContrast.R R/diffExp.R R/diffExpPerCluster.R R/dottedCase.R R/droplevels2.R R/encode.R R/enrichedGeneSets.R R/euclidean.R R/excludeContaminatedCells.R R/excludeNonCancerCells.R R/excludeNonHumanCells.R R/excludeProblematicCells.R R/export.R R/factorize.R R/filterCells.R R/filterNested.R R/findMarkers.R R/foldChangeToLogRatio.R R/fpkm.R R/geneFusions.R R/geneIds.R R/geneNames.R R/geneSet.R R/geneSetNames.R R/geneSetResults.R R/geometricMean.R R/headtail.R R/humanize.R R/import.R R/integerCounts.R R/interestingGroups.R R/intersectAll.R R/intersectionMatrix.R R/join.R R/kebabCase.R R/keepOnlyAtomicCols.R R/leadingEdge.R R/lfcShrink.R R/lfcShrinkType.R R/lfcThreshold.R R/logRatioToFoldChange.R R/makeDimnames.R R/makeLabel.R R/makeNames.R R/makeSampleData.R R/makeTitle.R R/makeWords.R R/mapCells.R R/mapColnames.R R/mapGenes.R R/mapGenesToIds.R R/mapGenesToRownames.R R/mapGenesToSymbols.R R/mapRownames.R R/markdownPlots.R R/markdownTables.R R/matchAll.R R/matchCellColumn.R R/matchGeneColumn.R R/matchNested.R R/matchRownameColumn.R R/matchSampleColumn.R R/matchTranscriptColumn.R R/melt.R R/metadata2.R R/metrics.R R/metricsPerSample.R R/mutate.R R/mutations.R R/nesThreshold.R R/nonzeroRowsAndCols.R R/package.R R/plot5Prime3PrimeBias.R R/plotBarcodeRanks.R R/plotBaseMean.R R/plotCellCounts.R R/plotCellCountsPerCluster.R R/plotCellTypesPerCluster.R R/plotCells.R R/plotCleveland.R R/plotContrastScatter.R R/plotCorrelation.R R/plotCorrelationHeatmap.R R/plotCountDensity.R R/plotCounts.R R/plotCountsCorrelation.R R/plotCountsCorrelationHeatmap.R R/plotCountsPerBiotype.R R/plotCountsPerBroadClass.R R/plotCountsPerCell.R R/plotCountsPerFeature.R R/plotCountsVsFeatures.R R/plotDegHeatmap.R R/plotDegPca.R R/plotDegStackedBar.R R/plotDegUpset.R R/plotDots.R R/plotEnrichedGeneSets.R R/plotEnrichedUpset.R R/plotExonicMappingRate.R R/plotFeature.R R/plotFeatureSaturation.R R/plotFeaturesDetected.R R/plotFeaturesPerCell.R R/plotGenderMarkers.R R/plotGeneEffect.R R/plotGeneEffectVsExpression.R R/plotGeneSet.R R/plotHeatmap.R R/plotIntergenicMappingRate.R R/plotIntronicMappingRate.R R/plotKnownMarkers.R R/plotLfc.R R/plotMa.R R/plotMappedReads.R R/plotMappingRate.R R/plotMarker.R R/plotMeanSd.R R/plotMitoRatio.R R/plotMitoVsCoding.R R/plotNes.R R/plotNovelty.R R/plotPcElbow.R R/plotPca.R R/plotPcaCovariates.R R/plotPseudoVsAlignedCounts.R R/plotQc.R R/plotQuantileHeatmap.R R/plotReadCountsPerCell.R R/plotReducedDim.R R/plotRrnaMappingRate.R R/plotStackedBarPlot.R R/plotSums.R R/plotTopGeneEffectPerCell.R R/plotTopGeneEffectPerGroup.R R/plotTopMarkers.R R/plotTotalCounts.R R/plotTotalReads.R R/plotTsne.R R/plotUmap.R R/plotUpset.R R/plotViolin.R R/plotVolcano.R R/plotWaterfall.R R/plotZerosVsDepth.R R/predictSensitivity.R R/rankedMatrix.R R/rbindToDataFrame.R R/relativeLogExpression.R R/removeNa.R R/results.R R/resultsDiff.R R/resultsMatrix.R R/resultsNames.R R/resultsTables.R R/sampleData.R R/sanitizeNa.R R/sanitizePercent.R R/select.R R/selectCells.R R/selectSamples.R R/sem.R R/sentenceCase.R R/showHeader.R R/slotAlignedCounts.R R/snakeCase.R R/splitByLevel.R R/standardizeCells.R R/stripExonVersions.R R/stripGeneVersions.R R/stripTranscriptVersions.R R/subsetPerSample.R R/tmm.R R/tnbc.R R/topCellsPerSample.R R/topMarkers.R R/tpm.R R/transcriptIds.R R/transcriptNames.R R/transformType.R R/unfactorize.R R/uniteInterestingGroups.R R/unlist2.R R/unnest2.R R/upperCamelCase.R R/zerosVsDepth.R R/zscore.R README.md man/AcidGenerics-package.Rd man/EnsemblToNcbi.Rd man/GeneToSymbol.Rd man/KnownMarkers.Rd man/NcbiToEnsembl.Rd man/TxToGene.Rd man/aggregateCellsToSamples.Rd man/aggregateCols.Rd man/aggregateRows.Rd man/alphaSummary.Rd man/alphaThreshold.Rd man/as.DESeqDataSet.Rd man/as.DESeqTransform.Rd man/as.DGEList.Rd man/as.DataFrame.Rd man/as.Seurat.Rd man/as.SingleCellExperiment.Rd man/as.SummarizedExperiment.Rd man/atomize.Rd man/autopadZeros.Rd man/barcodeRanksPerSample.Rd man/baseMeanThreshold.Rd man/calculateMetrics.Rd man/camelCase.Rd man/capitalize.Rd man/cast.Rd man/cellCountsPerCluster.Rd man/cellToSample.Rd man/cellTypesPerCluster.Rd man/cellsPerGeneFusion.Rd man/cellsPerMutation.Rd man/clusters.Rd man/coerceToList.Rd man/collapseToString.Rd man/collectionNames.Rd man/contrastName.Rd man/contrastNames.Rd man/contrastSamples.Rd man/convertGenesToSymbols.Rd man/convertSampleIdsToNames.Rd man/convertSymbolsToGenes.Rd man/convertToHuman.Rd man/convertTranscriptsToGenes.Rd man/correlation.Rd man/cpm.Rd man/deg.Rd man/degIntersection.Rd man/degPerContrast.Rd man/diffExp.Rd man/diffExpPerCluster.Rd man/dottedCase.Rd man/droplevels2.Rd man/encode.Rd man/enrichedGeneSets.Rd man/euclidean.Rd man/excludeContaminatedCells.Rd man/excludeNonCancerCells.Rd man/excludeNonHumanCells.Rd man/excludeProblematicCells.Rd man/export.Rd man/factorize.Rd man/filterCells.Rd man/filterNested.Rd man/findMarkers.Rd man/foldChangeToLogRatio.Rd man/fpkm.Rd man/geneFusions.Rd man/geneIds.Rd man/geneNames.Rd man/geneSet.Rd man/geneSetNames.Rd man/geneSetResults.Rd man/geometricMean.Rd man/headtail.Rd man/humanize.Rd man/import.Rd man/integerCounts.Rd man/interestingGroups.Rd man/intersectAll.Rd man/intersectionMatrix.Rd man/join.Rd man/kebabCase.Rd man/keepOnlyAtomicCols.Rd man/leadingEdge.Rd man/lfcShrink.Rd man/lfcShrinkType.Rd man/lfcThreshold.Rd man/logRatioToFoldChange.Rd man/makeDimnames.Rd man/makeLabel.Rd man/makeNames.Rd man/makeSampleData.Rd man/makeTitle.Rd man/makeWords.Rd man/mapCells.Rd man/mapColnames.Rd man/mapGenes.Rd man/mapGenesToIds.Rd man/mapGenesToRownames.Rd man/mapGenesToSymbols.Rd man/mapRownames.Rd man/markdownPlots.Rd man/markdownTables.Rd man/matchAll.Rd man/matchCellColumn.Rd man/matchGeneColumn.Rd man/matchNested.Rd man/matchRownameColumn.Rd man/matchSampleColumn.Rd man/matchTranscriptColumn.Rd man/melt.Rd man/metadata2.Rd man/metrics.Rd man/metricsPerSample.Rd man/mutate.Rd man/mutations.Rd man/nesThreshold.Rd man/nonzeroRowsAndCols.Rd man/plot5Prime3PrimeBias.Rd man/plotBarcodeRanks.Rd man/plotBaseMean.Rd man/plotCellCounts.Rd man/plotCellCountsPerCluster.Rd man/plotCellTypesPerCluster.Rd man/plotCells.Rd man/plotCleveland.Rd man/plotContrastScatter.Rd man/plotCorrelation.Rd man/plotCorrelationHeatmap.Rd man/plotCountDensity.Rd man/plotCounts.Rd man/plotCountsCorrelation.Rd man/plotCountsCorrelationHeatmap.Rd man/plotCountsPerBiotype.Rd man/plotCountsPerBroadClass.Rd man/plotCountsPerCell.Rd man/plotCountsPerFeature.Rd man/plotCountsVsFeatures.Rd man/plotDegHeatmap.Rd man/plotDegPca.Rd man/plotDegStackedBar.Rd man/plotDegUpset.Rd man/plotDots.Rd man/plotEnrichedGeneSets.Rd man/plotEnrichedUpset.Rd man/plotExonicMappingRate.Rd man/plotFeature.Rd man/plotFeatureSaturation.Rd man/plotFeaturesDetected.Rd man/plotFeaturesPerCell.Rd man/plotGenderMarkers.Rd man/plotGeneEffect.Rd man/plotGeneEffectVsExpression.Rd man/plotGeneSet.Rd man/plotHeatmap.Rd man/plotIntergenicMappingRate.Rd man/plotIntronicMappingRate.Rd man/plotKnownMarkers.Rd man/plotLfc.Rd man/plotMa.Rd man/plotMappedReads.Rd man/plotMappingRate.Rd man/plotMarker.Rd man/plotMeanSd.Rd man/plotMitoRatio.Rd man/plotMitoVsCoding.Rd man/plotNes.Rd man/plotNovelty.Rd man/plotPcElbow.Rd man/plotPca.Rd man/plotPcaCovariates.Rd man/plotPseudoVsAlignedCounts.Rd man/plotQc.Rd man/plotQuantileHeatmap.Rd man/plotReadsPerCell.Rd man/plotReducedDim.Rd man/plotRrnaMappingRate.Rd man/plotStackedBarPlot.Rd man/plotSums.Rd man/plotTopGeneEffectPerCell.Rd man/plotTopGeneEffectPerGroup.Rd man/plotTopMarkers.Rd man/plotTotalCounts.Rd man/plotTotalReads.Rd man/plotTsne.Rd man/plotUmap.Rd man/plotUpset.Rd man/plotViolin.Rd man/plotVolcano.Rd man/plotWaterfall.Rd man/plotZerosVsDepth.Rd man/predictSensitivity.Rd man/rankedMatrix.Rd man/rbindToDataFrame.Rd man/relativeLogExpression.Rd man/removeNa.Rd man/results.Rd man/resultsDiff.Rd man/resultsMatrix.Rd man/resultsNames.Rd man/resultsTables.Rd man/sampleData.Rd man/sanitizeNa.Rd man/sanitizePercent.Rd man/select.Rd man/selectCells.Rd man/selectSamples.Rd man/sem.Rd man/sentenceCase.Rd man/showHeader.Rd man/slotAlignedCounts.Rd man/snakeCase.Rd man/splitByLevel.Rd man/standardizeCells.Rd man/stripExonVersions.Rd man/stripGeneVersions.Rd man/stripTranscriptVersions.Rd man/subsetPerSample.Rd man/tmm.Rd man/tnbc.Rd man/topCellsPerSample.Rd man/topMarkers.Rd man/tpm.Rd man/transcriptIds.Rd man/transcriptNames.Rd man/transformType.Rd man/unfactorize.Rd man/uniteInterestingGroups.Rd man/unlist2.Rd man/unnest2.Rd man/upperCamelCase.Rd man/zerosVsDepth.Rd man/zscore.Rd