Function reference

All functions

GSEAHeatmap()

Plot GSEA results on a heatmap

MetadataSummary() plot(<nmf_metadata_summary>) MetadataHeatmap()

Summarize contribution of sample groups to NMF factors

RankPlot()

Plot NMF cross-validation results

RunGSEA()

Run Gene Set Enrichment Analysis on a Reduction

RunLNMF() MetadataPlot() GetSharedFactors() GetUniqueFactors()

Run Linked NMF on a Seurat object

RunNMF()

Run NMF on a Seurat object

ard_nmf()

Automatic Rank Determination NMF

cross_validate_nmf() plot(<cross_validate_nmf_data>)

Determine best rank for NMF using cross-validation

get_pbmc3k_data()

Load the pbmc3k dataset

pbmc3k

Compressed form of pbmc3k dataset

run_linked_nmf()

Run Linked Non-negative Matrix Factorization

run_nmf()

Run Non-negative Matrix Factorization

singlet singlet-package

Singlet