Files in C3BI-pasteur-fr/UTechSCB-SCHNAPPs
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md
.gitignore
.gitlab-ci.yml
CONTRIBUTING.md
DESCRIPTION
LICENSE.txt
NAMESPACE
R/DotPlotwithModuleScore.R R/cleanHistoryPath.R R/schnapps-Lite.R R/schnapps-Main.R
R/sysdata.rda
R/zzz.R README.md SCENIC-test.Rmd
SCHNAPPs.Rproj
_pkgdown.yml
data/scEx.RData
doc/Readme.R doc/Readme.Rmd
doc/Readme.html
docs/.nojekyll
docs/404.html
docs/CONTRIBUTING.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/Readme.html
docs/articles/index.html
docs/articles/pkdown/FAQs.html
docs/articles/pkdown/FAQs_files/vembedr-0.1.5/css/vembedr.css
docs/articles/pkdown/SCHNAPPs_usage.html
docs/articles/pkdown/SeuratWorkflow.html
docs/articles/pkdown/SeuratWorkflow_files/crosstalk-1.2.0/css/crosstalk.min.css
docs/articles/pkdown/SeuratWorkflow_files/crosstalk-1.2.0/js/crosstalk.js
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docs/articles/pkdown/SeuratWorkflow_files/datatables-binding-0.30/datatables.js
docs/articles/pkdown/SeuratWorkflow_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/pkdown/SeuratWorkflow_files/dt-core-1.13.4/css/jquery.dataTables.extra.css
docs/articles/pkdown/SeuratWorkflow_files/dt-core-1.13.4/css/jquery.dataTables.min.css
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docs/articles/pkdown/images/2Dzoomed.png
docs/articles/pkdown/images/2dAllGood.png
docs/articles/pkdown/images/2dCellDensity.png
docs/articles/pkdown/images/2dSeuratCluster.png
docs/articles/pkdown/images/2dplotAddOptions.png
docs/articles/pkdown/images/2dplotSmallGrp.png
docs/articles/pkdown/images/3dDEExpression.png
docs/articles/pkdown/images/CellSelection.png
docs/articles/pkdown/images/CellSelection2.png
docs/articles/pkdown/images/DataexplorationPanel.png
docs/articles/pkdown/images/SeuratNormalization.png
docs/articles/pkdown/images/alluvialAllGood.png
docs/articles/pkdown/images/alluvialSeurat.png
docs/articles/pkdown/images/beforeFilter.png
docs/articles/pkdown/images/beforeFilterApplied.png
docs/articles/pkdown/images/beforeFilterCellSelect.png
docs/articles/pkdown/images/beforeFilterCellsRM.png
docs/articles/pkdown/images/boxSelect.png
docs/articles/pkdown/images/cd8vscd4.png
docs/articles/pkdown/images/cellAddParam.png
docs/articles/pkdown/images/coexpresCl2Cl5.png
docs/articles/pkdown/images/coexpressionAll.png
docs/articles/pkdown/images/coexpressionSOM1.png
docs/articles/pkdown/images/coexpressionSOM2.png
docs/articles/pkdown/images/coexpressionSelected1.png
docs/articles/pkdown/images/coexpressionSelected2.png
docs/articles/pkdown/images/coexpressionSelected3.png
docs/articles/pkdown/images/coexpressionViolin1.png
docs/articles/pkdown/images/coexpressionViolin2.png
docs/articles/pkdown/images/dataexplorationExpression.png
docs/articles/pkdown/images/geneSelection.png
docs/articles/pkdown/images/geneSelection1.png
docs/articles/pkdown/images/geneSelection2.png
docs/articles/pkdown/images/geneSelectionRMGenes.png
docs/articles/pkdown/images/geneSelectionRegEx.png
docs/articles/pkdown/images/generalPC.png
docs/articles/pkdown/images/generalSample.png
docs/articles/pkdown/images/generalScater1.png
docs/articles/pkdown/images/generalScater2.png
docs/articles/pkdown/images/generalUMI.png
docs/articles/pkdown/images/groupedViolin.png
docs/articles/pkdown/images/heatmap1.png
docs/articles/pkdown/images/heatmap2.png
docs/articles/pkdown/images/heatmap3.png
docs/articles/pkdown/images/heatmapAllCells.png
docs/articles/pkdown/images/histogramDonor.png
docs/articles/pkdown/images/indivCells.png
docs/articles/pkdown/images/inputOptions.png
docs/articles/pkdown/images/loadSeurat.png
docs/articles/pkdown/images/loadingData.png
docs/articles/pkdown/images/nameGroupCell.png
docs/articles/pkdown/images/normByRP.png
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docs/articles/pkdown/images/parametersGeneral.png
docs/articles/pkdown/images/parametersNormalization.png
docs/articles/pkdown/images/parametersTSNE.png
docs/articles/pkdown/images/parametersUMAP.png
docs/articles/pkdown/images/scran_1.png
docs/articles/pkdown/images/scran_17.png
docs/articles/pkdown/images/scran_18.png
docs/articles/pkdown/images/scran_19.png
docs/articles/pkdown/images/scran_1a.png
docs/articles/pkdown/images/scran_1b.png
docs/articles/pkdown/images/scran_2.png
docs/articles/pkdown/images/scran_20.png
docs/articles/pkdown/images/scran_21.png
docs/articles/pkdown/images/selecteHighMT.png
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docs/articles/pkdown/images/setColor.png
docs/articles/pkdown/images/seuratGeneralParemeters.png
docs/articles/pkdown/images/showNames.png
docs/articles/pkdown/images/subclusteranalysis1.png
docs/articles/pkdown/images/subclusteranalysis2.png
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docs/reference/DotPlotwithModuleScore.html
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docs/reference/dot-schnappsEnv.html
docs/reference/index.html
docs/reference/scExOrg.html
docs/reference/schnapps.html
docs/reference/schnappsLite.html
docs/sitemap.xml
h.all.v2022.1.Hs.symbols.gmt
images/DE_expression.png
images/schnappsLogo.png
images2/2Dplot1.png
images2/2dplotAddOptions.png
images2/2dplotSmallGrp.png
images2/CellSelection.png
images2/DataexplorationPanel.png
images2/coexpressionAll.png
images2/coexpressionSOM1.png
images2/coexpressionSOM2.png
images2/coexpressionSelected1.png
images2/coexpressionSelected2.png
images2/coexpressionSelected3.png
images2/coexpressionVioloin1.png
images2/coexpressionVioloin2.png
images2/dataexplorationExpression.png
images2/geneSelection1.png
images2/geneSelection2.png
images2/generalPC.png
images2/generalSample.png
images2/generalScater1.png
images2/generalScater2.png
images2/generalUMI.png
images2/heatmap1.png
images2/heatmap2.png
images2/heatmap3.png
images2/loadingData.png
images2/overview.png
images2/parametersGeneral.png
images2/parametersNormalization.png
images2/parametersTSNE.png
images2/parametersUMAP.png
images2/subclusteranalysis1.png
images2/subclusteranalysis2.png
images2/table1.png
images2/tableAll.png
images2/tableReorder.png
images2/tableSelect2.png
images2/test.png
inst/app/Readme.txt
inst/app/applySimpleR.R inst/app/contributions/DE_DataExploration/outputs.R inst/app/contributions/DE_DataExploration/panelPlotFactFunc.R inst/app/contributions/DE_DataExploration/parameters.R inst/app/contributions/DE_DataExploration/reactives.R inst/app/contributions/DE_DataExploration/ui.R inst/app/contributions/LIANA/install.Rmd inst/app/contributions/LIANA/outputs.R inst/app/contributions/LIANA/reactives.R inst/app/contributions/LIANA/ui.R inst/app/contributions/coE_coExpression/outputs.R inst/app/contributions/coE_coExpression/reactives.R inst/app/contributions/coE_coExpression/ui.R inst/app/contributions/gQC_generalQC/outputs.R inst/app/contributions/gQC_generalQC/reactives.R inst/app/contributions/gQC_generalQC/ui.R inst/app/contributions/sCA_subClusterAnalysis/outputs.R inst/app/contributions/sCA_subClusterAnalysis/reactives.R inst/app/contributions/sCA_subClusterAnalysis/ui.R inst/app/controlbarContext.R inst/app/controlbarObservers.R inst/app/convert2scTK.R inst/app/defaultValues.R
inst/app/geneLists.RData
inst/app/moduleServer.R inst/app/modulesUI.R inst/app/outputs.R inst/app/parameters.R inst/app/reactives-lite.R inst/app/reactives.R inst/app/runDevApp.R inst/app/runVMApp.R inst/app/server-lite.R inst/app/server.R inst/app/serverFunctions.R inst/app/shortCuts.R inst/app/shortCuts.def.R inst/app/shortCutsTab.R inst/app/tabs.R inst/app/toolTips.R inst/app/ui-lite.R inst/app/ui.R
inst/develo/2dos.txt
inst/develo/BaderLabExampleMouseBrain.R inst/develo/DotPlotwithModuleScore.devel.R inst/develo/Readme.Rmd inst/develo/SamyExp1Special.R inst/develo/Untitled.R inst/develo/Untitled2.R inst/develo/VirtualBoxVM/app.R
inst/develo/VirtualBoxVM/shiny-server.conf
inst/develo/add2history
inst/develo/bookmarkDev.R inst/develo/cellchat.dev.R inst/develo/cellcycle.R inst/develo/changeVarName.R
inst/develo/changeVariables.txt
inst/develo/chatGPT.R inst/develo/checkInstall.R inst/develo/combineDataSetsPrototype.R inst/develo/convert2v2.R inst/develo/createData.Rmd
inst/develo/dockerCelia/Dockerfile
inst/develo/dockerCelia/DockerfileUpdate.txt
inst/develo/dockerCelia/app.R
inst/develo/dockerCelia/docker-compose.yml
inst/develo/dockerCelia/intro.Rmd
inst/develo/dockerCelia/intro.html
inst/develo/dockerCelia/runCelia.R inst/develo/dockerCelia/runCelia1.R inst/develo/dockerCelia/runDockerApp.R
inst/develo/dockerCelia/shiny-server.conf
inst/develo/dockerImage/Dockerfile
inst/develo/dockerImage/DockerfileUpdate.txt
inst/develo/dockerImage/app.R
inst/develo/dockerImage/docker-compose.yml
inst/develo/dockerImage/intro.Rmd inst/develo/dockerImage/runDockerApp.R
inst/develo/dockerImage/scExLite.RData
inst/develo/dockerImage/shiny-server.conf
inst/develo/dockerImage/shiny-server.sh
inst/develo/doubleViolinPlot.R inst/develo/ensg2symbol.R inst/develo/freezeReactiveValueExample.R inst/develo/georacle.R inst/develo/heatMapBIG.Rmd
inst/develo/human_cycle_markers.rds
inst/develo/install.maestro.R inst/develo/installSchnapps.R inst/develo/liana.cell.cell.comm.R inst/develo/licenses.Rmd
inst/develo/licensesList.txt
inst/develo/markdown/children/child.tartour.anova.Rmd inst/develo/markdown/customReportFromHistory.Rmd inst/develo/metaCell.Rmd inst/develo/metaCell.scEx.Rmd inst/develo/monocle3.wkfl.R
inst/develo/mouse_cycle_markers.rds
inst/develo/pairwiseCorrelation.R inst/develo/parallel.seurat.findmarkers.R inst/develo/parallel.sran.findmarkers.R inst/develo/params-tests.R inst/develo/phateR.R inst/develo/plotlyHover.R inst/develo/plotlyProxy.R inst/develo/prepSCHNAPPsInput.R inst/develo/prepWithinVM.R inst/develo/responsiveR.R inst/develo/rmdShiny.Rmd inst/develo/runLite.R inst/develo/scDEAsummary.Rmd inst/develo/scPipe.Levraud.Marsseq.R inst/develo/scenicDev.R inst/develo/seb2Schnapps.R inst/develo/singleR-MM.R inst/develo/startPaper.R inst/develo/startSchnapps.R inst/develo/test.Parallel.tsne.R
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inst/exampledata/scEx.csv
inst/exampledata/scExCells.csv
inst/exampledata/scExGenes.csv
inst/extdata/generalSCHNAPPs.html
inst/extdata/inputHelpIJS.txt
inst/extdata/possibleDefaultValues.R
inst/extdata/twoDselectedAddOptHelpIJS.txt
inst/testData/featureData.rdata
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inst/www/images/2dViolin.png
inst/www/images/3DClusterTsne.png
inst/www/images/3DExpressionGene.png
inst/www/images/3DUMAP.png
inst/www/images/Empty.png
inst/www/images/HistogramNormby.png
inst/www/images/HistogramSelected.png
inst/www/images/PanelPlotUMI.png
inst/www/images/PanelPlottSNE.png
inst/www/images/UMAPwParameters.png
inst/www/images/UMIhistogram.png
inst/www/images/VariancePCs.png
inst/www/images/ViolinCobinations.png
inst/www/images/ViolinPlotGeneCount.png
inst/www/images/VolcanoPlot.png
inst/www/images/WINDdendrogram.png
inst/www/images/barCodeVsGene.png
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inst/www/images/dotPlotGeneSets.png
inst/www/images/dotPlotGeneSetsMscore.png
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inst/www/images/heatmap.png
inst/www/images/logo.32.32.png
inst/www/images/logo.png
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inst/www/images/wkfl.png
inst/www/screen_shots.md
logo.png
man/DotPlotwithModuleScore.Rd man/dot-schnappsEnv.Rd man/scExOrg.Rd man/schnapps.Rd man/schnappsLite.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
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pkgdown/favicon/favicon-32x32.png
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scEx1.RData
test.Rmd
test.gmt
tests/testthat.R tests/testthat/_snaps/SCHNAPPs.md tests/testthat/_snaps/SCHNAPPs.new.md tests/testthat/pcaFunc.tests.R tests/testthat/serverFunctionstests.R tests/testthat/test-SCHNAPPs.R
vignettes/.gitignore
vignettes/Readme.Rmd vignettes/pkdown/FAQs.Rmd
vignettes/pkdown/GeneralQC.cRmd
vignettes/pkdown/SCHNAPPs_usage.Rmd vignettes/pkdown/SeuratWorkflow.Rmd vignettes/pkdown/addFunctionality2SCHNAPPs.Rmd
vignettes/pkdown/images/2Dplot1.png
vignettes/pkdown/images/2Dzoomed.png
vignettes/pkdown/images/2dAllGood.png
vignettes/pkdown/images/2dCellDensity.png
vignettes/pkdown/images/2dSeuratCluster.png
vignettes/pkdown/images/2dplotAddOptions.png
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vignettes/pkdown/images/3dDEExpression.png
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vignettes/pkdown/images/DataexplorationPanel.png
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vignettes/pkdown/images/alluvialAllGood.png
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vignettes/pkdown/images/boxSelect.png
vignettes/pkdown/images/cd8vscd4.png
vignettes/pkdown/images/cellAddParam.png
vignettes/pkdown/images/coExpressionAllclusters.mp4
vignettes/pkdown/images/coexpresCl2Cl5.png
vignettes/pkdown/images/coexpressionAll.png
vignettes/pkdown/images/coexpressionSOM1.png
vignettes/pkdown/images/coexpressionSOM2.png
vignettes/pkdown/images/coexpressionSelected1.png
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vignettes/pkdown/images/coexpressionSelected4.png
vignettes/pkdown/images/coexpressionViolin1.png
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vignettes/pkdown/images/scran_7.png
vignettes/pkdown/images/scran_8.png
vignettes/pkdown/images/scran_9.png
vignettes/pkdown/images/selecteHighMT.png
vignettes/pkdown/images/selectionSeurat.png
vignettes/pkdown/images/setColor.png
vignettes/pkdown/images/seuratGeneralParemeters.png
vignettes/pkdown/images/showNames.png
vignettes/pkdown/images/subclusteranalysis1.png
vignettes/pkdown/images/subclusteranalysis2.png
vignettes/pkdown/images/summaryStatsSeurat.png
vignettes/pkdown/images/table1.png
vignettes/pkdown/images/tableAll.png
vignettes/pkdown/images/tableReorder.png
vignettes/pkdown/images/tableSelect2.png
vignettes/pkdown/images/violinPermutation.png
vignettes/pkdown/images/zoom.png
vignettes/pkdown/images/zoomedSelection.png
vignettes/pkdown/ref.bib
vignettes/pkdown/scran.grunPancreas.RData
vignettes/pkdown/scranWorkflow.Rmd
vignettes/pkdown/seurat.pbmc.RData
C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on March 27, 2024, 2:40 a.m.