├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── datasets.R ├── main.R ├── rotations.R ├── seurat_utils.R └── utils.R ├── README.md ├── data ├── Hs2Mm.convert.table.RData ├── cell.cycle.obj.RData └── query_example_seurat.RData ├── docs ├── CSI_Toolkit.png ├── Proj_modes.png ├── RSticker_ProjecTILS.png ├── _config.yml ├── functions.md ├── projectils_logo_B_square.png ├── projectils_logo_W_square.png └── recalc_embeddings.png ├── inst └── extdata │ ├── reference_links.R │ └── reference_links.csv └── man ├── FindAllMarkers.bygroup.Rd ├── Hs2Mm.convert.table.Rd ├── ProjecTILs.classifier.Rd ├── Run.ProjecTILs.Rd ├── cell.cycle.obj.Rd ├── cellstate.predict.Rd ├── celltype.heatmap.Rd ├── compute_silhouette.Rd ├── find.discriminant.dimensions.Rd ├── find.discriminant.genes.Rd ├── get.reference.maps.Rd ├── list.reference.maps.Rd ├── load.reference.map.Rd ├── make.projection.Rd ├── make.reference.Rd ├── merge.Seurat.embeddings.Rd ├── plot.discriminant.3d.Rd ├── plot.projection.Rd ├── 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