/RSoptSC

Cell-cell communication and lineage inference for scRNA-seq data

Primary LanguageROtherNOASSERTION

RSoptSC

Build Status

Updates

Installation

install.packages("devtools")
library(devtools)
install_github("mkarikom/RSoptSC")

Features

  • Inference of cell-cell communication between single cells

  • Integration of multiple analyses in a consistent mathematical framework: clustering, marker genes, pseudotime, and lineage inference

  • Cell-cell similarity matrix construction to improve clustering

  • NMF-based marker gene identification

  • Prediction of the number of clusters present (via eigengap properties of the similarity matrix)

  • Prediction of the initial cell in pseudotime

Documentation

Full details of RSoptSC and examples are available here.