An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization originally described into Gambardella et al. 2019.
New functionalities implemented into the version 2 of GFICF package can be found in the preprint Pellecchia et al. 2022
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)