Files in singleCellTK

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

README.md

NEWS

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

data/sceBatches.rda

data/msigdb_table.rda

data/SEG.rda

data/mouseBrainSubsetSCE.rda

data/scExample.rda

R/importAnnData.R R/runBatchCorrection.R R/runDEAnalysis.R R/exportSCEtoAnndata.R R/GSVA.R R/sctkQCUtils.R R/reticulate_setup.R R/importMultipleSources.R R/scds_doubletdetection.R R/runQC.R R/scran_modelGeneVar.R R/plotSCEHeatmap.R

R/sysdata.rda

R/importDropEst.R R/convertGeneIDs.R R/getTopHVG.R R/findMarkerDiffExp.R R/plotBatchVariance.R R/ggPerQCWrapper.R R/getCluster.R R/importOptimus.R R/plotMarkerDiffExp.R R/DownsampleMatrix.R R/exportSCEtoTXT.R R/singleCellTK.R R/dropletUtils_emptyDrops.R R/importSeqc.R R/visPlot.R R/featureIndex.R R/plotBiomarker.R R/scater_logNormCounts.R R/scran_doubletCells.R R/readSingleCellMatrix.R R/doubletFinder_doubletDetection.R R/importSTARSolo.R R/plotDEAnalysis.R R/enrichRSCE.R R/importExampleData.R R/getUMAP.R R/scrublet_doubletDetection.R R/importGeneSets.R R/importBUStools.R R/plotPCA.R R/descriptions.R R/computeZScore.R R/decorate.R R/htmlReports.R R/plotTSNE.R R/mergeSCEColData.R R/dropletUtils_barcodeRank.R R/subsetSCE.R R/celda_decontX.R R/data.R R/getTSNE.R R/combineSCE.R R/miscFunctions.R R/ggPlotting.R R/getBiomarker.R R/scater_addPerCellQC.R R/importCellRanger.R R/sce2adata.R R/plotUMAP.R R/sampleSummaryStats.R R/getPCA.R R/seuratFunctions.R R/importFromFiles.R R/trimCounts.R vignettes/singleCellTK.Rmd man/plotSCEDensity.Rd man/runLimmaDE.Rd man/runCxdsBcdsHybrid.Rd man/seuratRunTSNE.Rd man/plotSCEBarColData.Rd man/runMAST.Rd man/runMNNCorrect.Rd man/exportSCE.Rd man/computeZScore.Rd man/runDropletQC.Rd man/dot-sce2adata.Rd man/plotBarcodeRankDropsResults.Rd man/seuratScaleData.Rd man/findMarkerDiffExp.Rd man/mouseBrainSubsetSCE.Rd man/combineSCE.Rd man/plotDoubletCellsResults.Rd man/plotSCEBarAssayData.Rd man/getMSigDBTable.Rd man/seuratComputeHeatmap.Rd man/discreteColorPalette.Rd man/importExampleData.Rd man/dot-getComponentNames.Rd man/generateMeta.Rd man/plotEmptyDropsScatter.Rd man/importFromFiles.Rd man/runBarcodeRankDrops.Rd man/runBcds.Rd man/runDEAnalysis.Rd man/seuratICA.Rd man/seuratNormalizeData.Rd man/seuratElbowPlot.Rd man/runDecontX.Rd man/seuratJackStrawPlot.Rd man/plotScdsHybridResults.Rd man/trimCounts.Rd man/reportCellQC.Rd man/selectSCTKConda.Rd man/plotDecontXResults.Rd man/importCellRangerV2Sample.Rd man/getUMAP.Rd man/SEG.Rd man/importAnnData.Rd man/dot-ggScatter.Rd man/calcEffectSizes.Rd man/sce.Rd man/plotSCEHeatmap.Rd man/plotSCEViolinColData.Rd man/importGeneSetsFromCollection.Rd man/importGeneSetsFromMSigDB.Rd man/runComBat.Rd man/seuratRunUMAP.Rd man/sampleSummaryStats.Rd man/downSampleDepth.Rd man/seuratFindHVG.Rd man/exportSCEtoFlatFile.Rd man/dot-checkDiffExpResultExists.Rd man/plotBiomarker.Rd man/subDiffEx.Rd man/plotDoubletFinderResults.Rd man/importMultipleSources.Rd man/plotPCA.Rd man/plotTSNE.Rd man/runDESeq2.Rd man/runBBKNN.Rd man/plotRunPerCellQCResults.Rd man/runDoubletCells.Rd man/importSEQC.Rd man/runCellQC.Rd man/plotSCEDensityColData.Rd man/plotDEGHeatmap.Rd man/runSCANORAMA.Rd man/seuratPCA.Rd man/convertSeuratToSCE.Rd man/plotDEGViolin.Rd man/runScrublet.Rd man/plotMASTThresholdGenes.Rd man/runSCMerge.Rd man/runScranSNN.Rd man/getBiomarker.Rd man/constructSCE.Rd man/sctkPythonInstallVirtualEnv.Rd man/seuratSCTransform.Rd man/iterateSimulations.Rd man/scater_logNormCounts.Rd man/plotDEGRegression.Rd man/dot-ggBar.Rd man/summarizeSCE.Rd man/runPerCellQC.Rd man/importDropEst.Rd man/getSceParams.Rd man/sctkListGeneSetCollections.Rd man/importCellRangerV3Sample.Rd man/enrichRSCE.Rd man/runCxds.Rd man/readSingleCellMatrix.Rd man/downSampleCells.Rd man/dot-seuratGetVariableFeatures.Rd man/qcInputProcess.Rd man/convertSCEToSeurat.Rd man/sceBatches.Rd man/seuratPlotHVG.Rd man/seuratReductionPlot.Rd man/reportDropletQC.Rd man/seuratIntegration.Rd man/dot-formatDEAList.Rd man/seuratFindClusters.Rd man/runLimmaBC.Rd man/plotBcdsResults.Rd man/importOptimus.Rd man/convertGeneIDs.Rd man/generateSimulatedData.Rd man/importBUStools.Rd man/getTSNE.Rd man/plotSCEScatter.Rd man/runDoubletFinder.Rd man/visPlot.Rd man/importSTARsolo.Rd man/msigdb_table.Rd man/featureIndex.Rd man/seuratHeatmapPlot.Rd man/plotEmptyDropsResults.Rd man/singleCellTK.Rd man/plotScrubletResults.Rd man/plotMarkerDiffExp.Rd man/importGeneSetsFromGMT.Rd man/plotSCEViolin.Rd man/dot-ggViolin.Rd man/getPCA.Rd man/getTopHVG.Rd man/subsetSCECols.Rd man/plotBarcodeRankScatter.Rd man/runEmptyDrops.Rd man/runKMeans.Rd man/dot-ggDensity.Rd man/scran_modelGeneVar.Rd man/retrieveSCEIndex.Rd man/dot-seuratInvalidate.Rd man/plotSCEBatchFeatureMean.Rd man/plotUMAP.Rd man/plotCxdsResults.Rd man/plotSCEDimReduceFeatures.Rd man/sctkPythonInstallConda.Rd man/dot-computeSignificantPC.Rd man/reportDiffExp.Rd man/plotSCEViolinAssayData.Rd man/dot-addSeuratToMetaDataSCE.Rd man/runFastMNN.Rd man/importGeneSetsFromList.Rd man/seuratComputeJackStraw.Rd man/runZINBWaVE.Rd man/dot-extractSCEAnnotation.Rd man/distinctColors.Rd man/reportQCTool.Rd man/mergeSCEColData.Rd man/simpleLog.Rd man/subsetSCERows.Rd man/plotBatchVariance.Rd man/plotSCEDimReduceColData.Rd man/exportSCEtoAnnData.Rd man/dot-updateAssaySCE.Rd man/gsvaSCE.Rd man/importCellRanger.Rd man/selectSCTKVirtualEnvironment.Rd man/runANOVA.Rd man/plotSCEDensityAssayData.Rd man/dataAnnotationColor.Rd

exec/mitochondrial_human_ensemble.gmt

exec/mitochondrial_human_ensemble_with_transcriptID.gmt

exec/SCTK_runQC.R exec/SCTK_runQC_Documentation.md

exec/mitochondrial_human_symbol.gmt

exec/SCTK_runQC_Documentation2.md tests/testthat.R tests/spelling.R tests/testthat/test-mergeColData.R tests/testthat/test-import.R tests/testthat/test-misc.R tests/testthat/test-qc.R tests/testthat/test-decontX.R tests/testthat/test-dropletUtils.R

inst/WORDLIST

inst/doc/singleCellTK.Rmd inst/doc/singleCellTK.R

inst/doc/singleCellTK.html

inst/shiny/ui_02_filter.R inst/shiny/ui_06_2_enrichR.R inst/shiny/shinyDirectoryInput.R inst/shiny/partials.R inst/shiny/ui_09_2_seuratWorkflow.R inst/shiny/ui_03_2_cluster.R

inst/shiny/styles.CSS

inst/shiny/colourGroupInput.R inst/shiny/ui_05_2_findMarker.R inst/shiny/ui_01_rowAnnotation.R inst/shiny/ui_09_3_celdaWorkflow.R inst/shiny/ui_05_1_diffex.R inst/shiny/ui_01_import.R inst/shiny/ui_04_batchcorrect.R inst/shiny/ui_02_qc.R inst/shiny/ui_01_columnAnnotation.R inst/shiny/ui_09_curatedworkflows.R inst/shiny/ui.R inst/shiny/ui_07_subsample.R inst/shiny/ui_08_2_cellviewer.R inst/shiny/ui_08_3_heatmap.R inst/shiny/server.R inst/shiny/helpers.R inst/shiny/ui_06_1_pathway.R inst/shiny/ui_02_qc_filter.R inst/shiny/ui_04_fs_dimred.R inst/shiny/ui_01_gene_sets.R inst/shiny/ui_celda.R inst/shiny/ui_export.R

inst/shiny/www/bu_bioinfo_logo.png

inst/shiny/www/ajax-loader-bar.gif

inst/shiny/www/bu_logo.PNG

inst/shiny/www/cbm.PNG

inst/shiny/www/bootstrap.min.css

inst/shiny/www/footer.html

inst/shiny/qc_help_pages/ui_cxds_help.R inst/shiny/qc_help_pages/ui_scrublet_help.R inst/shiny/qc_help_pages/ui_dc_and_qcm_help.R inst/shiny/qc_help_pages/ui_bcds_help.R inst/shiny/qc_help_pages/ui_doubletFinder_help.R inst/shiny/qc_help_pages/ui_decontX_help.R inst/shiny/qc_help_pages/ui_cxds_bcds_hybrid_help.R

inst/extdata/mito_subset.gmt

inst/extdata/hgmm_1k_v3_20x20/outs/filtered_feature_bc_matrix/barcodes.tsv.gz

inst/extdata/hgmm_1k_v3_20x20/outs/filtered_feature_bc_matrix/features.tsv.gz

inst/extdata/hgmm_1k_v3_20x20/outs/filtered_feature_bc_matrix/matrix.mtx.gz

inst/extdata/pbmc_1k_50x50/pbmc_1k_sparse_counts_barcodes.csv

inst/extdata/pbmc_1k_50x50/pbmc_1k_sparse_counts_genes.csv

inst/extdata/pbmc_1k_50x50/pbmc_1k_sparse_molecule_counts.mtx

inst/extdata/annData_pbmc_3k/pbmc3k_20by20.h5ad

inst/extdata/pbmc_4k_v2_20x20/outs/filtered_gene_bc_matrices/GRCh38/barcodes.tsv

inst/extdata/pbmc_4k_v2_20x20/outs/filtered_gene_bc_matrices/GRCh38/matrix.mtx

inst/extdata/pbmc_4k_v2_20x20/outs/filtered_gene_bc_matrices/GRCh38/genes.tsv

inst/extdata/BUStools_PBMC_1k_v3_20x20/genecount/genes.genes.txt

inst/extdata/BUStools_PBMC_1k_v3_20x20/genecount/genes.mtx

inst/extdata/BUStools_PBMC_1k_v3_20x20/genecount/genes.barcodes.txt

inst/extdata/Optimus_20x1000/call-MergeCellMetrics/merged-cell-metrics.csv.gz

inst/extdata/Optimus_20x1000/call-MergeGeneMetrics/merged-gene-metrics.csv.gz

inst/extdata/Optimus_20x1000/call-MergeCountFiles/sparse_counts_col_index.npy

inst/extdata/Optimus_20x1000/call-MergeCountFiles/sparse_counts.npz

inst/extdata/Optimus_20x1000/call-MergeCountFiles/sparse_counts_row_index.npy

inst/extdata/Optimus_20x1000/call-RunEmptyDrops/empty_drops_result.csv

inst/extdata/dropEst_scg71/cell.counts.rds

inst/extdata/STARsolo_PBMC_1k_v3_20x20/Gene/filtered/features.tsv

inst/extdata/STARsolo_PBMC_1k_v3_20x20/Gene/filtered/barcodes.tsv

inst/extdata/STARsolo_PBMC_1k_v3_20x20/Gene/filtered/matrix.mtx

inst/rmarkdown/qc/QCMetrics.Rmd inst/rmarkdown/qc/DecontX.Rmd inst/rmarkdown/qc/CxdsBcdsHybrid.Rmd inst/rmarkdown/qc/BarcodeRankDrops.Rmd inst/rmarkdown/qc/Scrublet.Rmd inst/rmarkdown/qc/EmptyDrops.Rmd inst/rmarkdown/qc/DropletQC.Rmd inst/rmarkdown/qc/DoubletFinder.Rmd inst/rmarkdown/qc/CellQC.Rmd inst/rmarkdown/qc/Cxds.Rmd inst/rmarkdown/qc/DoubletCells.Rmd inst/rmarkdown/qc/Bcds.Rmd

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.