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.
Examples & Functionality:
- Install GFICF package
- Getting Started
- Single-cell Gene Set Enrichement Analysis (scGSEA)
- Single-cell Mapper (scMAP)
- Batch Effect Correction (Cooming soon)