Files in ibseq/scs-analysis
Tools for Single Cell Genomics
.Rbuildignore
.gitattributes
.github/ISSUE_TEMPLATE/analysis-question.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/documentation.md
.github/ISSUE_TEMPLATE/feature-request.md
.github/no-response.yml
.github/pull_request_template.md
.github/workflows/R_CMD_check.yaml
.gitignore
.travis.yml
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/RcppExports.R
R/clustering.R
R/convenience.R
R/data.R
R/differential_expression.R
R/dimensional_reduction.R
R/generics.R
R/integration.R
R/mixscape.R
R/objects.R
R/preprocessing.R
R/reexports.R
R/tree.R
R/utilities.R
R/visualization.R
R/zfRenderSeurat.old
R/zzz.R
README.md
_pkgdown.yaml
appveyor.yml
azure-pipelines.yml
cran-comments.md
data/cc.genes.rda
data/cc.genes.updated.2019.rda
index.md
inst/CITATION
inst/extdata/pbmc_raw.txt
man/AddModuleScore.Rd
man/AggregateExpression.Rd
man/AnchorSet-class.Rd
man/AnnotateAnchors.Rd
man/Assay-class.Rd
man/AugmentPlot.Rd
man/AverageExpression.Rd
man/BGTextColor.Rd
man/BarcodeInflectionsPlot.Rd
man/BuildClusterTree.Rd
man/CalcPerturbSig.Rd
man/CalculateBarcodeInflections.Rd
man/CaseMatch.Rd
man/CellCycleScoring.Rd
man/CellScatter.Rd
man/CellSelector.Rd
man/Cells.Rd
man/CellsByImage.Rd
man/CollapseEmbeddingOutliers.Rd
man/CollapseSpeciesExpressionMatrix.Rd
man/ColorDimSplit.Rd
man/CombinePlots.Rd
man/CreateSCTAssayObject.Rd
man/CustomDistance.Rd
man/CustomPalette.Rd
man/DEenrichRPlot.Rd
man/DietSeurat.Rd
man/DimHeatmap.Rd
man/DimPlot.Rd
man/DimReduc-class.Rd
man/DiscretePalette.Rd
man/DoHeatmap.Rd
man/DotPlot.Rd
man/ElbowPlot.Rd
man/ExpMean.Rd
man/ExpSD.Rd
man/ExpVar.Rd
man/FastRowScale.Rd
man/FeaturePlot.Rd
man/FeatureScatter.Rd
man/FilterSlideSeq.Rd
man/FindAllMarkers.Rd
man/FindClusters.Rd
man/FindConservedMarkers.Rd
man/FindIntegrationAnchors.Rd
man/FindMarkers.Rd
man/FindMultiModalNeighbors.Rd
man/FindNeighbors.Rd
man/FindSpatiallyVariableFeatures.Rd
man/FindSubCluster.Rd
man/FindTransferAnchors.Rd
man/FindVariableFeatures.Rd
man/FoldChange.Rd
man/GetAssay.Rd
man/GetImage.Rd
man/GetIntegrationData.Rd
man/GetResidual.Rd
man/GetTissueCoordinates.Rd
man/GetTransferPredictions.Rd
man/Graph-class.Rd
man/GroupCorrelation.Rd
man/GroupCorrelationPlot.Rd
man/HTODemux.Rd
man/HTOHeatmap.Rd
man/HoverLocator.Rd
man/IFeaturePlot.Rd
man/ISpatialDimPlot.Rd
man/ISpatialFeaturePlot.Rd
man/IntegrateData.Rd
man/IntegrateEmbeddings.Rd
man/IntegrationAnchorSet-class.Rd
man/IntegrationData-class.Rd
man/JackStraw.Rd
man/JackStrawData-class.Rd
man/JackStrawPlot.Rd
man/L2CCA.Rd
man/L2Dim.Rd
man/LabelClusters.Rd
man/LabelPoints.Rd
man/LinkedPlots.Rd
man/Load10X_Spatial.Rd
man/LoadAnnoyIndex.Rd
man/LoadSTARmap.Rd
man/LocalStruct.Rd
man/LogNormalize.Rd
man/LogVMR.Rd
man/MULTIseqDemux.Rd
man/MapQuery.Rd
man/MappingScore.Rd
man/MetaFeature.Rd
man/MinMax.Rd
man/MixingMetric.Rd
man/MixscapeHeatmap.Rd
man/MixscapeLDA.Rd
man/ModalityWeights-class.Rd
man/NNPlot.Rd
man/Neighbor-class.Rd
man/NormalizeData.Rd
man/PCASigGenes.Rd
man/PercentageFeatureSet.Rd
man/PlotClusterTree.Rd
man/PlotPerturbScore.Rd
man/PolyDimPlot.Rd
man/PolyFeaturePlot.Rd
man/PredictAssay.Rd
man/PrepLDA.Rd
man/PrepSCTIntegration.Rd
man/ProjectDim.Rd
man/ProjectUMAP.Rd
man/Radius.Rd
man/Read10X.Rd
man/Read10X_Image.Rd
man/Read10X_h5.Rd
man/ReadSlideSeq.Rd
man/RegroupIdents.Rd
man/RelativeCounts.Rd
man/RenameCells.Rd
man/RidgePlot.Rd
man/RunCCA.Rd
man/RunICA.Rd
man/RunLDA.Rd
man/RunMarkVario.Rd
man/RunMixscape.Rd
man/RunMoransI.Rd
man/RunPCA.Rd
man/RunSPCA.Rd
man/RunTSNE.Rd
man/RunUMAP.Rd
man/SCTAssay-class.Rd
man/SCTResults.Rd
man/SCTransform.Rd
man/STARmap-class.Rd
man/SampleUMI.Rd
man/SaveAnnoyIndex.Rd
man/ScaleData.Rd
man/ScaleFactors.Rd
man/ScoreJackStraw.Rd
man/SelectIntegrationFeatures.Rd
man/SetIntegrationData.Rd
man/Seurat-class.Rd
man/Seurat-package.Rd
man/SeuratCommand-class.Rd
man/SeuratTheme.Rd
man/SlideSeq-class.Rd
man/SpatialImage-class.Rd
man/SpatialPlot.Rd
man/SplitObject.Rd
man/SubsetByBarcodeInflections.Rd
man/TopCells.Rd
man/TopFeatures.Rd
man/TopNeighbors.Rd
man/TransferAnchorSet-class.Rd
man/TransferData.Rd
man/UpdateSCTAssays.Rd
man/UpdateSymbolList.Rd
man/VariableFeaturePlot.Rd
man/VisiumV1-class.Rd
man/VizDimLoadings.Rd
man/VlnPlot.Rd
man/as.CellDataSet.Rd
man/as.Seurat.Rd
man/as.SingleCellExperiment.Rd
man/as.sparse.Rd
man/cc.genes.Rd
man/cc.genes.updated.2019.Rd
man/contrast-theory.Rd
man/merge.SCTAssay.Rd
man/reexports.Rd
man/subset.AnchorSet.Rd
seurat.Rproj
src/Makevars
src/ModularityOptimizer.cpp
src/ModularityOptimizer.h
src/RModularityOptimizer.cpp
src/RcppExports.cpp
src/data_manipulation.cpp
src/data_manipulation.h
src/fast_NN_dist.cpp
src/integration.cpp
src/integration.h
src/snn.cpp
src/snn.h
src/valid_pointer.c
tests/testdata/barcodes.tsv
tests/testdata/cr3.0/barcodes.tsv.gz
tests/testdata/cr3.0/features.tsv.gz
tests/testdata/cr3.0/matrix.mtx.gz
tests/testdata/genes.tsv
tests/testdata/matrix.mtx
tests/testdata/nbt_small.Rdata
tests/testdata/visium/filtered_feature_bc_matrix.h5
tests/testdata/visium/spatial/scalefactors_json.json
tests/testdata/visium/spatial/tissue_lowres_image.png
tests/testdata/visium/spatial/tissue_positions_list.csv
tests/testthat.R
tests/testthat/test_data_manipulation.R
tests/testthat/test_differential_expression.R
tests/testthat/test_dimensional_reduction.R
tests/testthat/test_integratedata.R
tests/testthat/test_integration.R
tests/testthat/test_load_10X.R
tests/testthat/test_modularity_optimizer.R
tests/testthat/test_objects.R
tests/testthat/test_preprocessing.R
tests/testthat/test_transferdata.R
tests/testthat/test_utilities.R
tests/testthat/test_visualization.R
travis_setup.sh
vignettes/archive.Rmd
vignettes/archive.yaml
vignettes/assets/anchorsb_2018.png
vignettes/assets/conversion_vignette.png
vignettes/assets/de_vignette.png
vignettes/assets/future_rocket.png
vignettes/assets/hashing_vignette.png
vignettes/assets/pbmc_dcs_cells.txt
vignettes/assets/pbmc_select.gif
vignettes/assets/sctransform.png
vignettes/assets/seurat_banner.jpg
vignettes/atacseq_integration_vignette.Rmd
vignettes/cell_cycle_vignette.Rmd
vignettes/conversion_vignette.Rmd
vignettes/de_vignette.Rmd
vignettes/dim_reduction_vignette.Rmd
vignettes/essential_commands.Rmd
vignettes/extensions.Rmd
vignettes/future_vignette.Rmd
vignettes/get_started.Rmd
vignettes/hashing_vignette.Rmd
vignettes/install.Rmd
vignettes/integration_introduction.Rmd
vignettes/integration_large_datasets.Rmd
vignettes/integration_mapping.Rmd
vignettes/integration_rpca.Rmd
vignettes/interaction_vignette.Rmd
vignettes/merge_vignette.Rmd
vignettes/mixscape_vignette.Rmd
vignettes/multimodal_reference_mapping.Rmd
vignettes/multimodal_vignette.Rmd
vignettes/pbmc3k_tutorial.Rmd
vignettes/sctransform_vignette.Rmd
vignettes/spatial_vignette.Rmd
vignettes/v4_changes.Rmd
vignettes/vignettes.yaml
vignettes/visualization_vignette.Rmd
vignettes/weighted_nearest_neighbor_analysis.Rmd
