BMILAB/scNPF: Pre-processing of single-cell RNA-seq data

scNPF is a R package for pre-processing of sing le-cell RNA-seq data by leveraging the context-specific topology inherent in the given data and the network information from priori gene-gene interaction networks. scNPF consists of two modules, including scNPF-propagation for imputing dropouts based on random walk with restart (RWR) and scNPF-fucion for fusing multiple smoothed expression matrices to a cell-cell similarity matrix. scNPF is highly integrative and flexible in that the two modules are independent but interconnected. scNPF can be used as a general and flexible pre-processing step prior to downstream analyses of scRNA-seq data for recovering gene expression lost, correcting gene expression measurements, and learning similarities between cells.

install.packages("remotes")
remotes::install_github("BMILAB/scNPF")