Files in satijalab/seurat-wrappers
Community-Provided Methods and Extensions for the Seurat Object
.DS_Store
.Rbuildignore
.github/no-response.yml
.github/workflows/test-vignettes.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/alevin.R
R/alra.R
R/banksy.R
R/cellbrowser.R
R/cogaps.R
R/conos.R
R/fast_mnn.R
R/fast_mnn_v5.R
R/glmpca.R
R/internal.R
R/liger.R
R/miqc.R
R/monocle3.R
R/pacmap.R
R/presto.R
R/scVI.R
R/tricycle.R
R/velocity.R
README.md
docs/README.md
docs/alevin.Rmd
docs/alevin.html
docs/alevin.md
docs/alra.Rmd
docs/alra.html
docs/alra.md
docs/alra_files/figure-markdown_github/explore-1.png
docs/banksy.Rmd
docs/banksy.md
docs/banksy_files/figure-gfm/hippo_gene-1.png
docs/banksy_files/figure-gfm/hippo_viz-1.png
docs/banksy_files/figure-gfm/hippo_viz-2.png
docs/banksy_files/figure-gfm/multi-spatial-1.png
docs/banksy_files/figure-gfm/multi-spatial-staggered-1.png
docs/banksy_files/figure-gfm/multi-umap-1.png
docs/banksy_files/figure-gfm/ss_markers-1.png
docs/banksy_files/figure-gfm/ss_viz-1.png
docs/cellbrowser.Rmd
docs/cellbrowser.html
docs/cellbrowser.md
docs/cellbrowser.png
docs/cipr.Rmd
docs/cipr.html
docs/cipr.md
docs/cipr_files/figure-gfm/unnamed-chunk-15-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-16-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-17-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-18-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-19-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-20-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-21-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-22-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-23-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-24-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-25-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-26-1.png
docs/cipr_files/figure-gfm/unnamed-chunk-9-1.png
docs/cogaps.html
docs/cogaps.md
docs/cogaps.rmd
docs/cogaps_files/figure-markdown_github/tenPatternsBVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/tenPatternsDcVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/tenPatternsFcgr3aVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/tenPatternsScatterPlot-1.png
docs/cogaps_files/figure-markdown_github/tenPatternsScatterPlot-2.png
docs/cogaps_files/figure-markdown_github/tenPatternsScatterPlot-3.png
docs/cogaps_files/figure-markdown_github/threePatternsExampleLympVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/threePatternsExampleMyeVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/threePatternsExampleScatterPlot-1.png
docs/cogaps_files/figure-markdown_github/threePatternsLymphoidVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/threePatternsMyeloidVlnPlot-1.png
docs/cogaps_files/figure-markdown_github/threePatternsScatterPlot-1.png
docs/conos.Rmd
docs/conos.html
docs/conos.md
docs/conos_files/figure-markdown_github/ifnb-1.png
docs/conos_files/figure-markdown_github/pancreas-1.png
docs/conos_files/figure-markdown_github/pbmcsca-1.png
docs/fast_mnn.Rmd
docs/fast_mnn.html
docs/fast_mnn.md
docs/fast_mnn_files/figure-gfm/ifnb_stim-1.png
docs/fast_mnn_files/figure-gfm/pancreas-1.png
docs/fast_mnn_files/figure-gfm/pbmcsca-1.png
docs/glmpca.Rmd
docs/glmpca.html
docs/glmpca.md
docs/glmpca_files/figure-markdown_github/explore-1.png
docs/glmpca_files/figure-markdown_github/explore2-1.png
docs/harmony.Rmd
docs/harmony.html
docs/harmony.md
docs/harmony_files/figure-markdown_github/ifnb_stim-1.png
docs/harmony_files/figure-markdown_github/pancreas-1.png
docs/harmony_files/figure-markdown_github/pbmcsca-1.png
docs/liger.Rmd
docs/liger.html
docs/liger.md
docs/liger_files/figure-gfm/ifnb-1.png
docs/liger_files/figure-gfm/pancreas-1.png
docs/liger_files/figure-gfm/pbmcsca-1.png
docs/miQC.Rmd
docs/miQC.html
docs/miQC.md
docs/miQC_files/figure-gfm/unnamed-chunk-10-1.png
docs/miQC_files/figure-gfm/unnamed-chunk-11-1.png
docs/miQC_files/figure-gfm/unnamed-chunk-2-1.png
docs/miQC_files/figure-gfm/unnamed-chunk-5-1.png
docs/miQC_files/figure-gfm/unnamed-chunk-6-1.png
docs/miQC_files/figure-gfm/unnamed-chunk-8-1.png
docs/miQC_files/figure-gfm/unnamed-chunk-9-1.png
docs/monocle3.Rmd
docs/monocle3.html
docs/monocle3.md
docs/monocle3_files/figure-gfm/dimreduc_hca-1.png
docs/monocle3_files/figure-gfm/integrated_dimplot-1.png
docs/monocle3_files/figure-gfm/monocle3_clustering-1.png
docs/monocle3_files/figure-gfm/pseudotime-1.png
docs/monocle3_files/figure-gfm/pseudotime-2.png
docs/monocle3_files/figure-gfm/subset_partitions-1.png
docs/nebulosa.Rmd
docs/nebulosa.html
docs/nebulosa.md
docs/nebulosa_files/figure-gfm/cd4_and_clustering-1.png
docs/nebulosa_files/figure-gfm/cd4_comparison-1.png
docs/nebulosa_files/figure-gfm/cd4_comparison-2.png
docs/nebulosa_files/figure-gfm/plot_cd3d-1.png
docs/nebulosa_files/figure-gfm/plot_cd4-1.png
docs/nebulosa_files/figure-gfm/unnamed-chunk-1-1.png
docs/nebulosa_files/figure-gfm/unnamed-chunk-2-1.png
docs/nebulosa_files/figure-gfm/unnamed-chunk-3-1.png
docs/nebulosa_files/figure-gfm/unnamed-chunk-4-1.png
docs/nebulosa_files/figure-gfm/unnamed-chunk-5-1.png
docs/pacmap.Rmd
docs/pacmap.html
docs/pacmap.md
docs/pacmap_files/figure-gfm/explore-1.png
docs/pacmap_files/figure-gfm/explore2-1.png
docs/pacmap_files/figure-gfm/pacmap_dim-1.png
docs/pacmap_files/figure-html/explore-1.png
docs/pacmap_files/figure-html/explore2-1.png
docs/pacmap_files/figure-html/pacmap_dim-1.png
docs/presto.html
docs/presto.md
docs/presto.rmd
docs/schex.Rmd
docs/schex.html
docs/schex.md
docs/schex_files/figure-markdown_github/plot-density-1.png
docs/schex_files/figure-markdown_github/plot-gene-1.png
docs/schex_files/figure-markdown_github/plot-meta-1-1.png
docs/schex_files/figure-markdown_github/plot-meta-2-1.png
docs/schex_files/figure-markdown_github/plot-meta-label-1.png
docs/scvelo.Rmd
docs/scvelo.html
docs/scvelo.md
docs/scvelo_files/figure-gfm/adata_plot_test-1.png
docs/scvelo_files/figure-gfm/latent_time-1.png
docs/scvelo_files/figure-gfm/latent_time-2.png
docs/scvelo_files/figure-gfm/matplotlib_test-1.png
docs/scvelo_files/figure-gfm/scvelo-1.png
docs/scvelo_files/figure-gfm/scvelo-2.png
docs/scvelo_files/figure-html/latent_time-1.png
docs/scvelo_files/figure-html/latent_time-2.png
docs/scvelo_files/figure-html/scvelo-1.png
docs/scvelo_files/figure-html/scvelo-2.png
docs/tricycle.Rmd
docs/tricycle.html
docs/tricycle.md
docs/tricycle_files/figure-gfm/density-1.png
docs/tricycle_files/figure-gfm/density-2.png
docs/tricycle_files/figure-gfm/loess-1.png
docs/tricycle_files/figure-gfm/plotemb-1.png
docs/velocity.Rmd
docs/velocity.html
docs/velocity.md
docs/velocity_files/figure-markdown_github/load_data-1.png
man/ALRAChooseKPlot.Rd
man/CellBrowser.Rd
man/FastMNNIntegration.Rd
man/LearnGraph.Rd
man/PlotMiQC.Rd
man/ReadAlevin.Rd
man/ReadVelocity.Rd
man/RunALRA.Rd
man/RunBanksy.Rd
man/RunCoGAPS.Rd
man/RunFastMNN.Rd
man/RunGLMPCA.Rd
man/RunMiQC.Rd
man/RunOptimizeALS.Rd
man/RunPaCMAP.Rd
man/RunPresto.Rd
man/RunPrestoAll.Rd
man/RunQuantileAlignSNF.Rd
man/RunQuantileNorm.Rd
man/RunSNF.Rd
man/RunVelocity.Rd
man/Runtricycle.Rd
man/SeuratWrappers-package.Rd
man/StopCellbrowser.Rd
man/VeloPlot.Rd
man/as.Seurat.extras.Rd
man/as.cell_data_set.Rd
man/findMatrix.Rd
man/scVIIntegration.Rd
man/writeSparseTsvChunks.Rd
seurat-wrappers.Rproj
test-vignettes.sh
