Files in dviraran/SingleR

Reference-based single-cell RNA-seq annotation

.github/ISSUE_TEMPLATE/please-post-issues-in-ltla-singler.md R/HelperFunctions.R R/SingleR.Create.R R/SingleR.Object.R R/SingleR.Plotting.R R/SingleR.R R/SingleR.References.R README.md SingleRbrowseR-standalone/app.R SingleRbrowseR-standalone/helpers.R man/Combine.Multiple.10X.Datasets.Rd man/CreateBigSingleRObject.Rd man/CreateSinglerObject.Rd man/CreateSinglerSeuratObject.Rd man/CreateVariableGeneSet.Rd man/ReadSingleCellData.Rd man/SingleR-class.Rd man/SingleR.Cluster.Rd man/SingleR.Combine.Rd man/SingleR.ConfidenceTest.Rd man/SingleR.CreateKangAnnotations.Rd man/SingleR.CreateObject.Rd man/SingleR.CreateSeurat.Rd man/SingleR.DrawBoxPlot.Rd man/SingleR.DrawHeatmap.Rd man/SingleR.DrawScatter.Rd man/SingleR.FineTune.Rd man/SingleR.PlotFeature.Rd man/SingleR.PlotTsne.Rd man/SingleR.Rd man/SingleR.ScoreData.Rd man/SingleR.Subset.Rd man/TPM.Rd man/blueprint_encode.Rd man/calculateSignatures.Rd man/cell.type.classification.Rd man/clusters.map.values.Rd man/convertSingleR2Browser.Rd man/fineTuningRound.Rd man/hpca.Rd man/human.egc.Rd man/human_lengths.Rd man/immgen.Rd man/medianMatrix.Rd man/mouse.egc.Rd man/mouse.rnaseq.Rd man/mouse_lengths.Rd man/quantileMatrix.Rd man/remove.Unnecessary.Data.single.Rd man/superRef.Rd manuscript_figures/FiguresData/Supp_Fig_6.pdf manuscript_figures/FiguresData/Supp_Fig_7.pdf manuscript_figures/FiguresOut/Fig1b_helft.validation.pdf manuscript_figures/FiguresOut/Fig1b_orig.ident.pdf manuscript_figures/FiguresOut/Fig1b_singler.annot.pdf manuscript_figures/FiguresOut/Fig1b_singler.heatmap.pdf manuscript_figures/FiguresOut/Fig1c-bcells-cd27.pdf manuscript_figures/FiguresOut/Fig1c-heatmap.pdf manuscript_figures/FiguresOut/Fig1c-seurat-clusters.pdf manuscript_figures/FiguresOut/Fig1c-singler-bcells.pdf manuscript_figures/FiguresOut/Fig1c-singler-legend.pdf manuscript_figures/FiguresOut/Fig1c-singler-tcells.pdf manuscript_figures/FiguresOut/Fig1c-singler.pdf manuscript_figures/FiguresOut/Fig1c-tcells-markers.pdf manuscript_figures/FiguresOut/Fig1c-tsne-clusters.pdf manuscript_figures/FiguresOut/Fig2a.pdf manuscript_figures/FiguresOut/Fig2a_legend.pdf manuscript_figures/FiguresOut/Fig2b-la.legened.pdf manuscript_figures/FiguresOut/Fig2b-la.pdf manuscript_figures/FiguresOut/Fig2c.pdf manuscript_figures/FiguresOut/Fig2c_legend.pdf manuscript_figures/FiguresOut/Fig2d-order.pdf manuscript_figures/FiguresOut/Fig2d.pdf manuscript_figures/FiguresOut/Fig3a-dendrogram.pdf manuscript_figures/FiguresOut/Fig3a-heatmap.pdf manuscript_figures/FiguresOut/Fig3a.legend.pdf manuscript_figures/FiguresOut/Fig3a.pdf manuscript_figures/FiguresOut/Fig3a_insert.pdf manuscript_figures/FiguresOut/Fig3b_1100001g20rik.pdf manuscript_figures/FiguresOut/Fig3b_Aif1.pdf manuscript_figures/FiguresOut/Fig3b_Apoe.pdf manuscript_figures/FiguresOut/Fig3b_Atp6v0d2.pdf manuscript_figures/FiguresOut/Fig3b_C1qa.pdf manuscript_figures/FiguresOut/Fig3b_C1qb.pdf manuscript_figures/FiguresOut/Fig3b_C1qc.pdf manuscript_figures/FiguresOut/Fig3b_Car4.pdf manuscript_figures/FiguresOut/Fig3b_Ccl9.pdf manuscript_figures/FiguresOut/Fig3b_Ccr2.pdf manuscript_figures/FiguresOut/Fig3b_Cdc42ep3.pdf manuscript_figures/FiguresOut/Fig3b_Chil3.pdf manuscript_figures/FiguresOut/Fig3b_Chil4.pdf manuscript_figures/FiguresOut/Fig3b_Cx3cr1.pdf manuscript_figures/FiguresOut/Fig3b_Cxcl16.pdf manuscript_figures/FiguresOut/Fig3b_Ear1.pdf manuscript_figures/FiguresOut/Fig3b_Ear10.pdf manuscript_figures/FiguresOut/Fig3b_Fabp1.pdf manuscript_figures/FiguresOut/Fig3b_Fabp4.pdf manuscript_figures/FiguresOut/Fig3b_H2-aa.pdf manuscript_figures/FiguresOut/Fig3b_H2-ab1.pdf manuscript_figures/FiguresOut/Fig3b_H2-eb1.pdf manuscript_figures/FiguresOut/Fig3b_Hexb.pdf manuscript_figures/FiguresOut/Fig3b_Il18.pdf manuscript_figures/FiguresOut/Fig3b_Il1b.pdf manuscript_figures/FiguresOut/Fig3b_Krt19.pdf manuscript_figures/FiguresOut/Fig3b_Krt79.pdf manuscript_figures/FiguresOut/Fig3b_Mafb.pdf manuscript_figures/FiguresOut/Fig3b_Marco.pdf manuscript_figures/FiguresOut/Fig3b_Mgl2.pdf manuscript_figures/FiguresOut/Fig3b_Mir5107.pdf manuscript_figures/FiguresOut/Fig3b_Mmp12.pdf manuscript_figures/FiguresOut/Fig3b_Plbd1.pdf manuscript_figures/FiguresOut/Fig3b_Plet1.pdf manuscript_figures/FiguresOut/Fig3b_S100a4.pdf manuscript_figures/FiguresOut/Fig3b_S100a6.pdf manuscript_figures/FiguresOut/Fig3b_Slpi.pdf manuscript_figures/FiguresOut/Fig3b_Socs3.pdf manuscript_figures/FiguresOut/Fig3b_Srgn.pdf manuscript_figures/FiguresOut/Fig3c.pdf manuscript_figures/FiguresOut/Fig3d-bulk.pdf manuscript_figures/FiguresOut/Fig3d.pdf manuscript_figures/FiguresOut/Fig4a.other-mouse-model-C3.pdf manuscript_figures/FiguresOut/Fig4a.other-mouse-model-C3genes.pdf manuscript_figures/FiguresOut/Fig4b-human.ipf.pdf manuscript_figures/FiguresOut/Fig5a.pdf manuscript_figures/FiguresOut/Fig5a_0days.pdf manuscript_figures/FiguresOut/Fig5a_14days.pdf manuscript_figures/FiguresOut/Fig5a_7days.pdf manuscript_figures/FiguresOut/Fig5b-tdtomata.pdf manuscript_figures/FiguresOut/Fig5c-cx3cr1.pdf manuscript_figures/FiguresOut/Fig6a-bulk-pdgfa.pdf manuscript_figures/FiguresOut/Fig6a-sc-pdgfa.pdf manuscript_figures/FiguresOut/Fig6b-tdtomata_pdgfa.pdf manuscript_figures/FiguresOut/Fig6c-migration.pdf manuscript_figures/FiguresOut/Fig6d-edu.2.pdf manuscript_figures/FiguresOut/Fig6d-edu.pdf manuscript_figures/FiguresOut/Fig6e.sc.fibs-boxplot.pdf manuscript_figures/FiguresOut/Fig6e.sc.fibs.pdf manuscript_figures/FiguresOut/Fig7a-Quantitation-pdgfra-pdgfrb.pdf manuscript_figures/FiguresOut/Fig7b.hydroxyproline.pdf manuscript_figures/FiguresOut/Fig7c.Quantitation_PDGFAA _in_CD68+_and_SH.pdf manuscript_figures/SingleR_ExtendedData.Rmd manuscript_figures/SingleR_ExtendedData.pdf manuscript_figures/figures.R vignettes/SingleR.MCA.Rmd vignettes/SingleR_create.Rmd vignettes/SingleR_specifications.Rmd vignettes/SingleR_specifications.pdf vignettes/SupplementaryInformation1.Rmd vignettes/SupplementaryInformation2.Rmd vignettes/simulation.R vignettes/simulations_functions.R