Files in compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

.BBSoptions

.Rbuildignore

.covrignore

.github/.gitignore

.github/workflows/BioC-check.yaml

.github/workflows/R-CMD-check.yaml

.gitignore

.travis.yml

DESCRIPTION

Dockerfile

LICENSE

NAMESPACE

NEWS.md R/DownsampleMatrix.R R/abundance.R R/allGenerics.R R/celda_decontX.R R/combineSCE.R R/computeHeatmap.R R/computeZScore.R R/data.R R/decorate.R R/descriptions.R R/detectCellOutlier.R R/doubletFinder_doubletDetection.R R/dropletUtils_barcodeRank.R R/dropletUtils_emptyDrops.R R/enrichRSCE.R R/exportSCEtoAnndata.R R/exportSCEtoTXT.R R/featureIndex.R R/getBiomarker.R R/getTopHVG.R R/ggPerQCWrapper.R R/ggPlotting.R R/htmlReports.R R/importAlevin.R R/importAnnData.R R/importBUStools.R R/importCellRanger.R R/importDropEst.R R/importExampleData.R R/importFromFiles.R R/importGeneSets.R R/importMultipleSources.R R/importOptimus.R R/importSTARSolo.R R/importSeqc.R R/mergeSCEColData.R R/miscFunctions.R R/plotBatchVariance.R R/plotBubble.R R/plotDEAnalysis.R R/plotDimRed.R R/plotFindMarkerHeatmap.R R/plotHeatmapMulti.R R/plotPCA.R R/plotPathway.R R/plotSCEHeatmap.R R/plotTSNE.R R/plotTopHVG.R R/plotUMAP.R R/readSingleCellMatrix.R R/reticulate_setup.R R/runBatchCorrection.R R/runCluster.R R/runClusterSummaryMetrics.R R/runDEAnalysis.R R/runDimReduce.R R/runFeatureSelection.R R/runFindMarker.R R/runGSVA.R R/runNormalization.R R/runPerCellQC.R R/runQC.R R/runQCUtils.R R/runSingleR.R R/runSoupX.R R/runTSCAN.R R/runTSNE.R R/runUMAP.R R/runVAM.R R/sampleSummaryStats.R R/scDblFinder_doubletDetection.R R/scanpyFunctions.R R/scater_CPM.R R/scater_PCA.R R/scater_logNormCounts.R R/scds_doubletdetection.R R/sce2adata.R R/scran_modelGeneVar.R R/scrublet_doubletDetection.R R/sctkQCUtils.R R/sctkTagging.R R/seuratFunctions.R R/singleCellTK.R R/subsetSCE.R

R/sysdata.rda

R/trimCounts.R R/validityFunctions.R README.md

_pkgdown.yml

data-raw/createMSigDB_SummaryTable.R data-raw/sctk_pbmc3k_analysis.R data-raw/sctk_pbmc3k_analysis_2.7.1.R

data/MitoGenes.rda

data/SEG.rda

data/mouseBrainSubsetSCE.rda

data/msigdb_table.rda

data/scExample.rda

data/sceBatches.rda

docs/32bit-R.png

docs/404.html

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inst/shiny/tests/shinytest/seuratUI.R inst/shiny/ui.R inst/shiny/ui_00_helloWorld.R inst/shiny/ui_01_columnAnnotation.R inst/shiny/ui_01_gene_sets.R inst/shiny/ui_01_import.R inst/shiny/ui_01_removeData.R inst/shiny/ui_01_rowAnnotation.R inst/shiny/ui_02_filter.R inst/shiny/ui_02_qc.R inst/shiny/ui_02_qc_filter.R inst/shiny/ui_03_2_cluster.R inst/shiny/ui_04_batchcorrect.R inst/shiny/ui_04_fs_dimred.R inst/shiny/ui_05_1_diffex.R inst/shiny/ui_05_2_findMarker.R inst/shiny/ui_05_3_cellTypeLabel.R inst/shiny/ui_06_1_pathway.R inst/shiny/ui_06_1_pathwayAnalysis.R inst/shiny/ui_06_2_enrichR.R inst/shiny/ui_07_subsample.R inst/shiny/ui_08_2_cellviewer.R inst/shiny/ui_08_3_heatmap.R inst/shiny/ui_08_4_bubbleplot.R inst/shiny/ui_09_2_seuratWorkflow.R inst/shiny/ui_09_3_celdaWorkflow.R inst/shiny/ui_09_4_scanpyWorkflow.R inst/shiny/ui_10_1_TSCAN.R inst/shiny/ui_export.R

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man/MitoGenes.Rd man/SEG.Rd man/calcEffectSizes.Rd man/combineSCE.Rd man/computeHeatmap.Rd man/computeZScore.Rd man/constructSCE.Rd man/convertSCEToSeurat.Rd man/convertSeuratToSCE.Rd man/dedupRowNames.Rd man/detectCellOutlier.Rd man/diffAbundanceFET.Rd man/discreteColorPalette.Rd man/distinctColors.Rd man/downSampleCells.Rd man/downSampleDepth.Rd man/expData-ANY-character-method.Rd man/expData-set-ANY-character-CharacterOrNullOrMissing-logical-method.Rd man/expData-set.Rd man/expData.Rd man/expDataNames-ANY-method.Rd man/expDataNames.Rd man/expDeleteDataTag.Rd man/expSetDataTag.Rd man/expTaggedData.Rd man/exportSCE.Rd man/exportSCEToSeurat.Rd man/exportSCEtoAnnData.Rd man/exportSCEtoFlatFile.Rd man/featureIndex.Rd man/generateHTANMeta.Rd man/generateMeta.Rd man/generateSimulatedData.Rd man/getBiomarker.Rd man/getDEGTopTable.Rd man/getDiffAbundanceResults.Rd man/getEnrichRResult.Rd man/getFindMarkerTopTable.Rd man/getGenesetNamesFromCollection.Rd man/getMSigDBTable.Rd man/getPathwayResultNames.Rd man/getSampleSummaryStatsTable.Rd man/getSceParams.Rd man/getSeuratVariableFeatures.Rd man/getSoupX.Rd man/getTSCANResults.Rd man/getTopHVG.Rd man/importAlevin.Rd man/importAnnData.Rd man/importBUStools.Rd man/importCellRanger.Rd man/importCellRangerV2Sample.Rd man/importCellRangerV3Sample.Rd man/importDropEst.Rd man/importExampleData.Rd man/importFromFiles.Rd man/importGeneSetsFromCollection.Rd man/importGeneSetsFromGMT.Rd man/importGeneSetsFromList.Rd man/importGeneSetsFromMSigDB.Rd man/importMitoGeneSet.Rd man/importMultipleSources.Rd man/importOptimus.Rd man/importSEQC.Rd man/importSTARsolo.Rd man/iterateSimulations.Rd man/listSampleSummaryStatsTables.Rd man/mergeSCEColData.Rd man/mouseBrainSubsetSCE.Rd man/msigdb_table.Rd man/plotBarcodeRankDropsResults.Rd man/plotBarcodeRankScatter.Rd man/plotBatchCorrCompare.Rd man/plotBatchVariance.Rd man/plotBcdsResults.Rd man/plotBubble.Rd man/plotClusterAbundance.Rd man/plotCxdsResults.Rd man/plotDEGHeatmap.Rd man/plotDEGRegression.Rd man/plotDEGViolin.Rd man/plotDEGVolcano.Rd man/plotDecontXResults.Rd man/plotDimRed.Rd man/plotDoubletFinderResults.Rd man/plotEmptyDropsResults.Rd man/plotEmptyDropsScatter.Rd man/plotFindMarkerHeatmap.Rd man/plotMASTThresholdGenes.Rd man/plotPCA.Rd man/plotPathway.Rd man/plotRunPerCellQCResults.Rd man/plotSCEBarAssayData.Rd man/plotSCEBarColData.Rd man/plotSCEBatchFeatureMean.Rd man/plotSCEDensity.Rd man/plotSCEDensityAssayData.Rd man/plotSCEDensityColData.Rd man/plotSCEDimReduceColData.Rd man/plotSCEDimReduceFeatures.Rd man/plotSCEHeatmap.Rd man/plotSCEScatter.Rd man/plotSCEViolin.Rd man/plotSCEViolinAssayData.Rd man/plotSCEViolinColData.Rd man/plotScDblFinderResults.Rd man/plotScanpyDotPlot.Rd man/plotScanpyEmbedding.Rd man/plotScanpyHVG.Rd man/plotScanpyHeatmap.Rd man/plotScanpyMarkerGenes.Rd man/plotScanpyMarkerGenesDotPlot.Rd man/plotScanpyMarkerGenesHeatmap.Rd man/plotScanpyMarkerGenesMatrixPlot.Rd man/plotScanpyMarkerGenesViolin.Rd man/plotScanpyMatrixPlot.Rd man/plotScanpyPCA.Rd man/plotScanpyPCAGeneRanking.Rd man/plotScanpyPCAVariance.Rd man/plotScanpyViolin.Rd man/plotScdsHybridResults.Rd man/plotScrubletResults.Rd man/plotSeuratElbow.Rd man/plotSeuratGenes.Rd man/plotSeuratHVG.Rd man/plotSeuratHeatmap.Rd man/plotSeuratJackStraw.Rd man/plotSeuratReduction.Rd man/plotSoupXResults.Rd man/plotTSCANClusterDEG.Rd man/plotTSCANClusterPseudo.Rd man/plotTSCANDimReduceFeatures.Rd man/plotTSCANPseudotimeGenes.Rd man/plotTSCANPseudotimeHeatmap.Rd man/plotTSCANResults.Rd man/plotTSNE.Rd man/plotTopHVG.Rd man/plotUMAP.Rd man/qcInputProcess.Rd man/readSingleCellMatrix.Rd man/reportCellQC.Rd man/reportClusterAbundance.Rd man/reportDiffAbundanceFET.Rd man/reportDiffExp.Rd man/reportDropletQC.Rd man/reportFindMarker.Rd man/reportQCTool.Rd man/reportSeurat.Rd man/reportSeuratClustering.Rd man/reportSeuratDimRed.Rd man/reportSeuratFeatureSelection.Rd man/reportSeuratMarkerSelection.Rd man/reportSeuratNormalization.Rd man/reportSeuratResults.Rd man/reportSeuratRun.Rd man/reportSeuratScaling.Rd man/retrieveSCEIndex.Rd man/runBBKNN.Rd man/runBarcodeRankDrops.Rd man/runBcds.Rd man/runCellQC.Rd man/runClusterSummaryMetrics.Rd man/runComBatSeq.Rd man/runCxds.Rd man/runCxdsBcdsHybrid.Rd man/runDEAnalysis.Rd man/runDecontX.Rd man/runDimReduce.Rd man/runDoubletFinder.Rd man/runDropletQC.Rd man/runEmptyDrops.Rd man/runEnrichR.Rd man/runFastMNN.Rd man/runFeatureSelection.Rd man/runFindMarker.Rd man/runGSVA.Rd man/runHarmony.Rd man/runKMeans.Rd man/runLimmaBC.Rd man/runMNNCorrect.Rd man/runModelGeneVar.Rd man/runNormalization.Rd man/runPerCellQC.Rd man/runSCANORAMA.Rd man/runSCMerge.Rd man/runScDblFinder.Rd man/runScanpyFindClusters.Rd man/runScanpyFindHVG.Rd man/runScanpyFindMarkers.Rd man/runScanpyNormalizeData.Rd man/runScanpyPCA.Rd man/runScanpyScaleData.Rd man/runScanpyTSNE.Rd man/runScanpyUMAP.Rd man/runScranSNN.Rd man/runScrublet.Rd man/runSeuratFindClusters.Rd man/runSeuratFindHVG.Rd man/runSeuratFindMarkers.Rd man/runSeuratHeatmap.Rd man/runSeuratICA.Rd man/runSeuratIntegration.Rd man/runSeuratJackStraw.Rd man/runSeuratNormalizeData.Rd man/runSeuratPCA.Rd man/runSeuratSCTransform.Rd man/runSeuratScaleData.Rd man/runSeuratTSNE.Rd man/runSeuratUMAP.Rd man/runSingleR.Rd man/runSoupX.Rd man/runTSCAN.Rd man/runTSCANClusterDEAnalysis.Rd man/runTSCANDEG.Rd man/runTSNE.Rd man/runUMAP.Rd man/runVAM.Rd man/runZINBWaVE.Rd man/sampleSummaryStats.Rd man/scaterCPM.Rd man/scaterPCA.Rd man/scaterlogNormCounts.Rd man/sce.Rd man/sceBatches.Rd man/sctkListGeneSetCollections.Rd man/sctkPythonInstallConda.Rd man/sctkPythonInstallVirtualEnv.Rd man/selectSCTKConda.Rd man/selectSCTKVirtualEnvironment.Rd man/setRowNames.Rd man/setSCTKDisplayRow.Rd man/singleCellTK.Rd man/subDiffEx.Rd man/subsetSCECols.Rd man/subsetSCERows.Rd man/summarizeSCE.Rd man/trimCounts.Rd

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vignettes/articles/ieee.csl

vignettes/articles/import_annotation.Rmd vignettes/articles/import_data.Rmd vignettes/articles/import_genesets.Rmd vignettes/articles/installation.Rmd vignettes/articles/normalization.Rmd vignettes/articles/pathwayAnalysis.Rmd

vignettes/articles/references.bib

vignettes/articles/scanpy_curated_workflow.Rmd vignettes/articles/seurat_curated_workflow.Rmd vignettes/articles/trajectoryAnalysis.Rmd vignettes/articles/ui_qc.Rmd vignettes/articles/visualization.Rmd vignettes/articles/webApp.Rmd vignettes/singleCellTK.R vignettes/singleCellTK.Rmd

vignettes/singleCellTK.html

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.

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compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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compbiomed/singleCellTK Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Files in compbiomed/singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data