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An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

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gficf v2 - Single-cell gene set enrichment analysis

Details on scGSEA and scMAP implemented into the version 2 of GFICF package can be found in the NAR genomics and bioinformatics manuscript Franchini et al. 2023

GFICF v1 manuscript can be found here at Gambardella et al. 2019.

The package also includes Phenograph Louvain method clustering using RcppAnnoy library from uwot and a naive but fast parallel implementation of Jaccard Coefficient estimation using RcppParallel. The package also include data reduction with either Principal Component Analisys (PCA) or non-negative matrix factorization RcppML before to apply t-SNE or UMAP for single cell data visualization.

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An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

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