├── .DS_Store ├── .Rbuildignore ├── .github ├── no-response.yml └── workflows │ └── test-vignettes.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── alevin.R ├── alra.R ├── banksy.R ├── cellbrowser.R ├── cogaps.R ├── conos.R ├── fast_mnn.R ├── fast_mnn_v5.R ├── glmpca.R ├── internal.R ├── liger.R ├── miqc.R ├── monocle3.R ├── pacmap.R ├── presto.R ├── scVI.R ├── tricycle.R └── velocity.R ├── README.md ├── docs ├── README.md ├── alevin.Rmd ├── alevin.html ├── alevin.md ├── alra.Rmd ├── alra.html ├── alra.md ├── alra_files │ └── figure-markdown_github │ │ └── explore-1.png ├── banksy.Rmd ├── banksy.md ├── banksy_files │ └── figure-gfm │ │ ├── hippo_gene-1.png │ │ ├── hippo_viz-1.png │ │ ├── hippo_viz-2.png │ │ ├── multi-spatial-1.png │ │ ├── multi-spatial-staggered-1.png │ │ ├── multi-umap-1.png │ │ ├── ss_markers-1.png │ │ └── ss_viz-1.png ├── cellbrowser.Rmd ├── cellbrowser.html ├── cellbrowser.md ├── cellbrowser.png ├── cipr.Rmd ├── cipr.html ├── cipr.md ├── cipr_files │ └── figure-gfm │ │ ├── unnamed-chunk-15-1.png │ │ ├── unnamed-chunk-16-1.png │ │ ├── unnamed-chunk-17-1.png │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-19-1.png │ │ ├── unnamed-chunk-20-1.png │ │ ├── unnamed-chunk-21-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-23-1.png │ │ ├── unnamed-chunk-24-1.png │ │ ├── unnamed-chunk-25-1.png │ │ ├── unnamed-chunk-26-1.png │ │ └── unnamed-chunk-9-1.png ├── cogaps.html ├── cogaps.md ├── cogaps.rmd ├── cogaps_files │ └── figure-markdown_github │ │ ├── tenPatternsBVlnPlot-1.png │ │ ├── tenPatternsDcVlnPlot-1.png │ │ ├── tenPatternsFcgr3aVlnPlot-1.png │ │ ├── tenPatternsScatterPlot-1.png │ │ ├── tenPatternsScatterPlot-2.png │ │ ├── tenPatternsScatterPlot-3.png │ │ ├── threePatternsExampleLympVlnPlot-1.png │ │ ├── threePatternsExampleMyeVlnPlot-1.png │ │ ├── threePatternsExampleScatterPlot-1.png │ │ ├── threePatternsLymphoidVlnPlot-1.png │ │ ├── threePatternsMyeloidVlnPlot-1.png │ │ └── threePatternsScatterPlot-1.png ├── conos.Rmd ├── conos.html ├── conos.md ├── conos_files │ └── figure-markdown_github │ │ ├── ifnb-1.png │ │ ├── pancreas-1.png │ │ └── pbmcsca-1.png ├── fast_mnn.Rmd ├── fast_mnn.html ├── fast_mnn.md ├── fast_mnn_files │ └── figure-gfm │ │ ├── ifnb_stim-1.png │ │ ├── pancreas-1.png │ │ └── pbmcsca-1.png ├── glmpca.Rmd ├── glmpca.html ├── glmpca.md ├── glmpca_files │ └── figure-markdown_github │ │ ├── explore-1.png │ │ └── explore2-1.png ├── harmony.Rmd ├── harmony.html ├── harmony.md ├── harmony_files │ └── figure-markdown_github │ │ ├── ifnb_stim-1.png │ │ ├── pancreas-1.png │ │ └── pbmcsca-1.png ├── liger.Rmd ├── liger.html ├── liger.md ├── liger_files │ └── figure-gfm │ │ ├── ifnb-1.png │ │ ├── pancreas-1.png │ │ └── pbmcsca-1.png ├── miQC.Rmd ├── miQC.html ├── miQC.md ├── miQC_files │ └── figure-gfm │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-5-1.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-8-1.png │ │ └── unnamed-chunk-9-1.png ├── monocle3.Rmd ├── monocle3.html ├── monocle3.md ├── monocle3_files │ └── figure-gfm │ │ ├── dimreduc_hca-1.png │ │ ├── integrated_dimplot-1.png │ │ ├── monocle3_clustering-1.png │ │ ├── pseudotime-1.png │ │ ├── pseudotime-2.png │ │ └── subset_partitions-1.png ├── nebulosa.Rmd ├── nebulosa.html ├── nebulosa.md ├── nebulosa_files │ └── figure-gfm │ │ ├── cd4_and_clustering-1.png │ │ ├── cd4_comparison-1.png │ │ ├── cd4_comparison-2.png │ │ ├── plot_cd3d-1.png │ │ ├── plot_cd4-1.png │ │ ├── unnamed-chunk-1-1.png │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-5-1.png ├── pacmap.Rmd ├── pacmap.html ├── pacmap.md ├── pacmap_files │ ├── figure-gfm │ │ ├── explore-1.png │ │ ├── explore2-1.png │ │ └── pacmap_dim-1.png │ └── figure-html │ │ ├── explore-1.png │ │ ├── explore2-1.png │ │ └── pacmap_dim-1.png ├── presto.html ├── presto.md ├── presto.rmd ├── schex.Rmd ├── schex.html ├── schex.md ├── schex_files │ └── figure-markdown_github │ │ ├── plot-density-1.png │ │ ├── plot-gene-1.png │ │ ├── plot-meta-1-1.png │ │ ├── plot-meta-2-1.png │ │ └── plot-meta-label-1.png ├── scvelo.Rmd ├── scvelo.html ├── scvelo.md ├── scvelo_files │ ├── figure-gfm │ │ ├── adata_plot_test-1.png │ │ ├── latent_time-1.png │ │ ├── latent_time-2.png │ │ ├── matplotlib_test-1.png │ │ ├── scvelo-1.png │ │ └── scvelo-2.png │ └── figure-html │ │ ├── latent_time-1.png │ │ ├── latent_time-2.png │ │ ├── scvelo-1.png │ │ └── scvelo-2.png ├── tricycle.Rmd ├── tricycle.html ├── tricycle.md ├── tricycle_files │ └── figure-gfm │ │ ├── density-1.png │ │ ├── density-2.png │ │ ├── loess-1.png │ │ └── plotemb-1.png ├── velocity.Rmd ├── velocity.html ├── velocity.md └── velocity_files │ └── figure-markdown_github │ └── load_data-1.png ├── man ├── ALRAChooseKPlot.Rd ├── CellBrowser.Rd ├── FastMNNIntegration.Rd ├── LearnGraph.Rd ├── PlotMiQC.Rd ├── ReadAlevin.Rd ├── ReadVelocity.Rd ├── RunALRA.Rd ├── RunBanksy.Rd ├── 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