Files in acidgenomics/AcidGenerics
Acid Genomics Generics
.Rbuildignore
.gitignore
.lintr
DESCRIPTION
LICENSE
NAMESPACE
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
_pkgdown.yml
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
package.Rproj
pkgdown/extra.css
todo.org
