├── .Rbuildignore ├── .gitignore ├── CODE_OF_CONDUCT.md ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── ProjectSVR.Rproj ├── R ├── cnmf.R ├── data.R ├── grid_cells.R ├── label_transfer.R ├── objects.R ├── projection.R ├── signature_score.R ├── themes.R ├── utils.R ├── visualization.R └── wrappers.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── data ├── pals.rda └── ribo.genes.rda ├── docs ├── 404.html ├── CODE_OF_CONDUCT.html ├── LICENSE-text.html ├── LICENSE.html ├── LOG.html ├── articles │ ├── index.html │ ├── mapQuery_ICB_BRCA.html │ ├── mapQuery_ICB_BRCA_files │ │ └── figure-html │ │ │ ├── alluvia_plot-1.png │ │ │ ├── box_plot-1.png │ │ │ ├── map_qc_plot-1.png │ │ │ ├── map_qc_plot-2.png │ │ │ ├── preference_plot-1.png │ │ │ ├── preference_plot2-1.png │ │ │ ├── projection_plot-1.png │ │ │ ├── reference_mapping-1.png │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── wilcoxon_test-1.png │ ├── mapQuery_Ythdc2-KO.html │ ├── mapQuery_Ythdc2-KO_files │ │ └── figure-html │ │ │ ├── alluvia_plot-1.png │ │ │ ├── majority_vote-1.png │ │ │ ├── map_quality-1.png │ │ │ ├── projection_plot-1.png │ │ │ └── reference_mapping-1.png │ ├── mapQuery_Zfp541-KO.html │ ├── mapQuery_Zfp541-KO_files │ │ └── figure-html │ │ │ ├── compare_heatmap-1.png │ │ │ ├── label_transfer-1.png │ │ │ ├── map_qc_plot-1.png │ │ │ ├── map_qc_plot-2.png │ │ │ ├── map_qc_threshold-1.png │ │ │ └── reference_mapping-1.png │ ├── mapQuery_immune_RPL.html │ ├── mapQuery_immune_RPL_files │ │ └── figure-html │ │ │ ├── alluvia_plot-1.png │ │ │ ├── compare_heatmap-1.png │ │ │ ├── label_transfer-1.png │ │ │ ├── map_quality-1.png │ │ │ ├── projection_plot-1.png │ │ │ ├── projection_plot_dNK-1.png │ │ │ └── reference_mapping-1.png │ ├── mapQuery_invitro_meiosis.html │ ├── mapQuery_invitro_meiosis_files │ │ └── figure-html │ │ │ ├── alluvia_plot-1.png │ │ │ ├── label_transfer-1.png │ │ │ ├── map_quality-1.png │ │ │ ├── pan_markers_plot-1.png │ │ │ ├── projection_plot-1.png │ │ │ ├── reference_mapping-1.png │ │ │ ├── unnamed-chunk-1-1.png │ │ │ └── unnamed-chunk-2-1.png │ ├── misc_Ythdc2-KO_pseudotime.html │ ├── misc_Ythdc2-KO_pseudotime_files │ │ └── figure-html │ │ │ ├── load_reference-1.png │ │ │ └── unnamed-chunk-1-1.png │ ├── misc_disco_pbmc_svm.html │ ├── misc_disco_pbmc_svm_files │ │ └── figure-html │ │ │ ├── auto_annotation-1.png │ │ │ ├── load_reference-1.png │ │ │ ├── markers-1.png │ │ │ └── visualization-1.png │ ├── model_mfia.html │ ├── model_mfia_files │ │ └── figure-html │ │ │ └── load_reference-1.png │ ├── model_mtca.html │ ├── model_mtca_files │ │ └── figure-html │ │ │ ├── feature_plot-1.png │ │ │ ├── meta_cells-1.png │ │ │ ├── meta_cells-2.png │ │ │ └── referenc_plot-1.png │ ├── model_pbmc.html │ ├── model_pbmc_files │ │ └── figure-html │ │ │ └── load_reference-1.png │ ├── model_pctl.html │ ├── model_pctl_files │ │ └── figure-html │ │ │ ├── add_gene_module_score-1.png │ │ │ ├── add_gene_module_score2-1.png │ │ │ ├── referenc_plot-1.png │ │ │ └── referenc_plot2-1.png │ ├── quick_start.html │ └── quick_start_files │ │ └── figure-html │ │ ├── add_gene_module_score-1.png │ │ ├── compare_heatmap-1.png │ │ ├── label_transfer-1.png │ │ ├── load_reference-1.png │ │ ├── map_qc_plot-1.png │ │ ├── map_qc_plot-2.png │ │ ├── map_qc_threshold-1.png │ │ ├── projection_plot-1.png │ │ └── reference_mapping-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── deps │ ├── bootstrap-5.1.3 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── data-deps.txt │ └── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── AbundanceTest.html │ ├── AddProjQual.html │ ├── AlluviaPlot-1.png │ ├── AlluviaPlot.html │ ├── BoxPlot.html │ ├── CellProject-class.html │ ├── ComputeModuleScore.html │ ├── CreateModelObject.html │ ├── CreateReference.html │ ├── DimTheme.html │ ├── EstimateKnnDensity.html │ ├── FindOptimalK.html │ ├── FitEnsemblMultiClassif.html │ ├── FitEnsembleSVM.html │ ├── GridDensity-class.html │ ├── GroupPreferencePlot-1.png │ ├── GroupPreferencePlot.html │ ├── KnnLabelTransfer.html │ ├── LabelTransfer.html │ ├── MajorityVote.html │ ├── MapQCPlot.html │ ├── MapQuery.html │ ├── MergeCells.html │ ├── NNHelper.html │ ├── PercentageStat.html │ ├── PlotProjection.html │ ├── PredictNewdata.html │ ├── ProjectNewdata.html │ ├── RefineProjection.html │ ├── Rplot001.png │ ├── RunCNMF.html │ ├── SplitCellProject.html │ ├── VolcanoPlot.html │ ├── cells.Neighbor.html │ ├── dot-hist2d.html │ ├── figures │ │ ├── ProjectSVR-logo.png │ │ ├── ProjectSVR-workflow.png │ │ ├── mean-knn-dist.png │ │ └── perturbed-gc-cnmf-k-selection.png │ ├── index.html │ ├── mcFindAllMarkers.html │ ├── merge.CellProject.html │ ├── newCellProject.html │ ├── pals.html │ ├── plot.GridDensity.html │ ├── ribo.genes.html │ ├── sknn.html │ ├── subset.GridDensity.html │ └── subset2.html ├── search.json └── sitemap.xml ├── man ├── AbundanceTest.Rd ├── AddProjQual.Rd ├── AlluviaPlot.Rd ├── BoxPlot.Rd ├── CellProject-class.Rd ├── ComputeModuleScore.Rd ├── CreateReference.Rd ├── DimTheme.Rd ├── EstimateKnnDensity.Rd ├── FindOptimalK.Rd ├── FitEnsemblMultiClassif.Rd ├── FitEnsembleSVM.Rd ├── GridDensity-class.Rd ├── GroupPreferencePlot.Rd ├── KnnLabelTransfer.Rd ├── LabelTransfer.Rd ├── MajorityVote.Rd ├── MapQCPlot.Rd ├── MapQuery.Rd ├── MergeCells.Rd ├── NNHelper.Rd ├── PercentageStat.Rd ├── PlotProjection.Rd ├── PredictNewdata.Rd ├── ProjectNewdata.Rd ├── RefineProjection.Rd ├── RunCNMF.Rd ├── SplitCellProject.Rd ├── VolcanoPlot.Rd ├── dot-hist2d.Rd ├── figures │ ├── ProjectSVR-logo.png │ ├── ProjectSVR-workflow.png │ └── mean-knn-dist.png ├── mcFindAllMarkers.Rd ├── merge.CellProject.Rd ├── newCellProject.Rd ├── pals.Rd ├── plot.GridDensity.Rd ├── ribo.genes.Rd ├── sknn.Rd ├── 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