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flscuts

Main functions used in flscuts

add_souporcell_seurat()
Add Souporcell Clustering Output to a Seurat Object
annotate_nhood()
Annotate Milo Neighborhoods with Cell Types
iterative_LSI()
Iterative Latent Semantic Indexing (LSI) for Single-Cell Data (Compatible with Monocle3 and Seurat) with optional UMAP
make_nhoods()
Make Milo Neighborhoods from Seurat Object
project_data()
Project Data into UMAP Embedding of Single-Cell Object (Compatible with Monocle3 and Seurat)
plot_projection()
Plot Projection of Projected Data onto Projector's UMAP Embedding (Compatible with Monocle3 and Seurat)
test_nhoods()
Test Milo Neighborhoods for Differential Abundance
find_markers()
Find Marker Genes for Differentially Abundant Neighborhoods
adt_dotplot()
Generate a Dot Plot with ADT Data from a Seurat Object
aml_panel()
Generate a Panel of Dot Plots for AML Markers

Additional functions

Helper functions to add or modify elements

monocle3_to_seurat()
Convert Monocle3 Cell Data Set to Seurat Object
seurat_to_monocle3()
Convert Seurat Object to Monocle3 Cell Data Set
files3_prep()
Find Cell Ranger Data Files