Files in acidgenomics/basejump
Base Functions for Bioinformatics

.Rbuildignore
.gitignore
.lintr
.travis.yml
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/AllClasses.R R/AllGenerics.R R/AllGlobals.R R/Ensembl2Entrez-methods.R R/Gene2Symbol-methods.R R/HGNC2Ensembl.R R/MGI2Ensembl.R R/Tx2Gene-methods.R R/aggregate-methods.R R/aggregateCellsToSamples-methods.R R/alphaThreshold-methods.R R/autopadZeros-methods.R R/calculateMetrics-methods.R R/camelCase-methods.R R/cell2sample-methods.R R/collapseToString-methods.R R/combine-methods.R R/convertGenesToSymbols-methods.R R/convertSampleIDsToNames-methods.R R/convertTranscriptsToGenes-methods.R R/correlation-methods.R R/counts-methods.R R/deprecated.R R/detectHPC.R R/detectLanes.R R/dottedCase-methods.R R/estimateSizeFactors-methods.R R/filterCells-methods.R R/geneNames-methods.R R/geneSynonyms.R R/genomeVersions.R R/geometricMean-methods.R R/headtail-methods.R R/humanize-methods.R R/importSampleData.R R/importTx2Gene.R R/imports.R R/interestingGroups-methods.R R/internal.R R/lfcThreshold-methods.R R/logRatio-methods.R R/makeGene2Symbol.R R/makeSampleData-methods.R R/makeSingleCellExperiment-methods.R R/makeSummarizedExperiment-methods.R R/makeTx2Gene.R R/makeTx2GeneFromFASTA.R R/mapCellsToSamples.R R/mapGenes-methods.R R/markdown-methods.R R/markdownHeader.R R/markdownLink.R R/markdownList.R R/markdownPlots.R R/markdownTables.R R/matchEnsemblReleaseToURL.R R/matchHumanOrthologs.R R/matchInterestingGroups.R R/matchesGene2Symbol.R R/matchesInterestingGroups.R R/mcolnames-methods.R R/melt-methods.R R/metrics-methods.R R/microplate.R R/minimalSampleData.R R/multiassignAsEnvir.R R/nonzeroRowsAndCols-methods.R R/organism-methods.R R/package.R R/prepareTemplate.R R/pseudobulk-methods.R R/rankedMatrix.R R/reexports-coerce.R R/reexports.R R/sampleData-methods.R R/sampleNames-methods.R R/sanitizeSampleData.R R/selectSamples-methods.R R/separator.R R/showHeader.R R/showSlotInfo.R R/sizeFactors-methods.R R/snakeCase-methods.R R/sortUnique.R R/stripTranscriptVersions-methods.R R/subsetPerSample-methods.R R/summary-methods.R R/toStringUnique.R R/topCellsPerSample-methods.R R/tpm-methods.R R/uniteInterestingGroups-methods.R R/upperCamelCase-methods.R R/zerosVsDepth-methods.R README.md
_pkgdown.yml
appveyor.yml
basejump.Rproj
data-raw/plotlist.R
docs/.DS_Store
docs/404.html
docs/CNAME
docs/CONTRIBUTING.html
docs/LICENSE-text.html
docs/articles/basejump.html
docs/articles/index.html
docs/authors.html
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docs/docsearch.js
docs/extra.css
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docs/pkgdown.css
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docs/reference/Ensembl2Entrez-class.html
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docs/reference/HGNC2Ensembl-class.html
docs/reference/HGNC2Ensembl.html
docs/reference/MGI2Ensembl-class.html
docs/reference/MGI2Ensembl.html
docs/reference/Tx2Gene-class.html
docs/reference/Tx2Gene.html
docs/reference/aggregate.html
docs/reference/aggregateCellsToSamples.html
docs/reference/alphaThreshold.html
docs/reference/autopadZeros.html
docs/reference/barcodePattern.html
docs/reference/basejump-package.html
docs/reference/basejumpTestsURL.html
docs/reference/calculateMetrics.html
docs/reference/camelCase.html
docs/reference/cell2sample.html
docs/reference/collapseToString.html
docs/reference/combine.html
docs/reference/convertGenesToSymbols.html
docs/reference/convertSampleIDsToNames.html
docs/reference/convertTranscriptsToGenes.html
docs/reference/counts.html
docs/reference/defunct.html
docs/reference/deprecated.html
docs/reference/detectHPC.html
docs/reference/detectLanes.html
docs/reference/dottedCase.html
docs/reference/estimateSizeFactors.html
docs/reference/filterCells.html
docs/reference/formalsList.html
docs/reference/geneNames.html
docs/reference/geneSynonyms.html
docs/reference/genomeMetadataNames.html
docs/reference/genomeVersions.html
docs/reference/geometricMean.html
docs/reference/headtail.html
docs/reference/humanize.html
docs/reference/importSampleData.html
docs/reference/importTx2Gene.html
docs/reference/index.html
docs/reference/interestingGroups.html
docs/reference/lanePattern.html
docs/reference/lfcThreshold.html
docs/reference/logRatio.html
docs/reference/makeGene2Symbol.html
docs/reference/makeSampleData.html
docs/reference/makeSingleCellExperiment.html
docs/reference/makeSummarizedExperiment.html
docs/reference/makeTx2Gene.html
docs/reference/makeTx2GeneFromFASTA.html
docs/reference/mapCellsToSamples.html
docs/reference/mapGenes.html
docs/reference/markdown.html
docs/reference/markdownHeader.html
docs/reference/markdownLink.html
docs/reference/markdownList.html
docs/reference/markdownPlots-1.png
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docs/reference/markdownPlots.html
docs/reference/markdownTables.html
docs/reference/matchEnsemblReleaseToURL.html
docs/reference/matchHumanOrthologs.html
docs/reference/matchInterestingGroups.html
docs/reference/matchesGene2Symbol.html
docs/reference/matchesInterestingGroups.html
docs/reference/mcolnames.html
docs/reference/melt.html
docs/reference/metadataBlacklist.html
docs/reference/metrics.html
docs/reference/metricsCols.html
docs/reference/microplate.html
docs/reference/minimalSampleData.html
docs/reference/multiassignAsEnvir.html
docs/reference/nonzeroRowsAndCols.html
docs/reference/organism.html
docs/reference/prepareTemplate.html
docs/reference/pseudobulk.html
docs/reference/rankedMatrix.html
docs/reference/reexports.html
docs/reference/sampleData.html
docs/reference/sampleNames.html
docs/reference/sanitizeSampleData.html
docs/reference/selectSamples.html
docs/reference/separator.html
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docs/reference/showSlotInfo.html
docs/reference/sizeFactors.html
docs/reference/snakeCase.html
docs/reference/sortUnique.html
docs/reference/stripTranscriptVersions.html
docs/reference/subsetPerSample.html
docs/reference/summary.html
docs/reference/toStringUnique.html
docs/reference/topCellsPerSample.html
docs/reference/tpm.html
docs/reference/uniteInterestingGroups.html
docs/reference/updateMessage.html
docs/reference/upperCamelCase.html
docs/reference/zerosVsDepth.html
inst/rmarkdown/shared/_footer.Rmd inst/rmarkdown/shared/_header.Rmd inst/rmarkdown/shared/_links.Rmd
inst/rmarkdown/shared/_output.yaml
inst/rmarkdown/shared/_setup.R
inst/rmarkdown/shared/bibliography.bib
man/Ensembl2Entrez-class.Rd man/Ensembl2Entrez.Rd man/Gene2Symbol-class.Rd man/Gene2Symbol.Rd man/HGNC2Ensembl-class.Rd man/HGNC2Ensembl.Rd man/MGI2Ensembl-class.Rd man/MGI2Ensembl.Rd man/Tx2Gene-class.Rd man/Tx2Gene.Rd man/aggregate.Rd man/aggregateCellsToSamples.Rd man/alphaThreshold.Rd man/autopadZeros.Rd man/barcodePattern.Rd man/basejump-package.Rd man/basejumpTestsURL.Rd man/calculateMetrics.Rd man/camelCase.Rd man/cell2sample.Rd man/collapseToString.Rd man/combine.Rd man/convertGenesToSymbols.Rd man/convertSampleIDsToNames.Rd man/convertTranscriptsToGenes.Rd man/correlation.Rd man/counts.Rd man/defunct.Rd man/deprecated.Rd man/detectHPC.Rd man/detectLanes.Rd man/dottedCase.Rd man/estimateSizeFactors.Rd man/filterCells.Rd man/formalsList.Rd man/geneNames.Rd man/geneSynonyms.Rd man/genomeMetadataNames.Rd man/genomeVersions.Rd man/geometricMean.Rd man/headtail.Rd man/humanize.Rd man/importSampleData.Rd man/importTx2Gene.Rd man/interestingGroups.Rd man/lanePattern.Rd man/lfcThreshold.Rd man/logRatio.Rd man/makeGene2Symbol.Rd man/makeSampleData.Rd man/makeSingleCellExperiment.Rd man/makeSummarizedExperiment.Rd man/makeTx2Gene.Rd man/makeTx2GeneFromFASTA.Rd man/mapCellsToSamples.Rd man/mapGenes.Rd man/markdown.Rd man/markdownHeader.Rd man/markdownLink.Rd man/markdownList.Rd man/markdownPlots.Rd man/markdownTables.Rd man/matchEnsemblReleaseToURL.Rd man/matchHumanOrthologs.Rd man/matchInterestingGroups.Rd man/matchesGene2Symbol.Rd man/matchesInterestingGroups.Rd man/mcolnames.Rd man/melt.Rd man/metadataBlacklist.Rd man/metrics.Rd man/metricsCols.Rd man/microplate.Rd man/minimalSampleData.Rd man/multiassignAsEnvir.Rd man/nonzeroRowsAndCols.Rd man/organism.Rd man/prepareTemplate.Rd man/pseudobulk.Rd man/rankedMatrix.Rd man/reexports.Rd man/sampleData.Rd man/sampleNames.Rd man/sanitizeSampleData.Rd man/selectSamples.Rd man/separator.Rd man/showHeader.Rd man/showSlotInfo.Rd man/sizeFactors.Rd man/snakeCase.Rd man/sortUnique.Rd man/stripTranscriptVersions.Rd man/subsetPerSample.Rd man/summary.Rd man/toStringUnique.Rd man/topCellsPerSample.Rd man/tpm.Rd man/uniteInterestingGroups.Rd man/updateMessage.Rd man/upperCamelCase.Rd man/zerosVsDepth.Rd
pkgdown/extra.css
tests/testthat-extra/test-geneSynonyms.R tests/testthat-extra/test-matchEnsemblReleaseToURL.R tests/testthat-extra/test-matchHumanOrthologs.R tests/testthat.R
tests/testthat/.gitignore
tests/testthat/helper-cache.R tests/testthat/helper-globals.R tests/testthat/test-Ensembl2Entrez.R tests/testthat/test-Gene2Symbol.R tests/testthat/test-HGNC2Ensembl.R tests/testthat/test-MGI2Ensembl.R tests/testthat/test-Tx2Gene.R tests/testthat/test-aggregate-SingleCellExperiment.R tests/testthat/test-aggregate.R tests/testthat/test-alphaThreshold.R tests/testthat/test-autopadZeros.R tests/testthat/test-calculateMetrics.R tests/testthat/test-cell2sample.R tests/testthat/test-collapseToString.R tests/testthat/test-combine.R tests/testthat/test-convertGenesToSymbols.R tests/testthat/test-convertSampleIDsToNames.R tests/testthat/test-convertTranscriptsToGenes.R tests/testthat/test-correlation.R tests/testthat/test-counts.R tests/testthat/test-detectHPC.R tests/testthat/test-detectLanes.R tests/testthat/test-detectOrganism.R tests/testthat/test-estimateSizeFactors.R tests/testthat/test-filterCells.R tests/testthat/test-geneNames.R tests/testthat/test-geneSynonyms.R tests/testthat/test-geometricMean.R tests/testthat/test-headtail.R tests/testthat/test-humanize.R tests/testthat/test-importSampleData.R tests/testthat/test-importTx2Gene.R tests/testthat/test-interestingGroups.R tests/testthat/test-lfcThreshold.R tests/testthat/test-logRatio.R tests/testthat/test-makeGene2Symbol.R tests/testthat/test-makeSampleData.R tests/testthat/test-makeSingleCellExperiment.R tests/testthat/test-makeSummarizedExperiment.R tests/testthat/test-makeTx2Gene.R tests/testthat/test-mapCellsToSamples.R tests/testthat/test-mapGenes.R tests/testthat/test-markdown.R tests/testthat/test-matchEnsemblReleaseToURL.R tests/testthat/test-matchHumanOrthologs.R tests/testthat/test-matchesGene2Symbol.R tests/testthat/test-matchesInterestingGroups.R tests/testthat/test-mcolnames.R tests/testthat/test-melt.R tests/testthat/test-metrics.R tests/testthat/test-microplate.R tests/testthat/test-minimalSampleData.R tests/testthat/test-multiassignAsEnvir.R tests/testthat/test-organism.R tests/testthat/test-printString.R tests/testthat/test-pseudobulk.R tests/testthat/test-rankedMatrix.R tests/testthat/test-removeNA.R tests/testthat/test-sampleData.R tests/testthat/test-sampleNames.R tests/testthat/test-sanitizeNA.R tests/testthat/test-sanitizeSampleData.R tests/testthat/test-selectSamples.R tests/testthat/test-separator.R tests/testthat/test-showSlotInfo.R tests/testthat/test-sortUnique.R tests/testthat/test-stripTranscriptVersions.R tests/testthat/test-subsetPerSample.R tests/testthat/test-syntactic.R tests/testthat/test-toStringUnique.R tests/testthat/test-topCellsPerSample.R tests/testthat/test-tpm.R tests/testthat/test-uniteInterestingGroups.R tests/testthat/test-zerosVsDepth.R tests/testthat/text-matchInterestingGroups.R
vignettes/.gitignore
vignettes/basejump.Rmd
acidgenomics/basejump documentation built on Nov. 12, 2019, 8:49 a.m.