mkarikom / RSoptSC

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

RSoptSC

Updates

• Demo SoptSC at vignette("Joost_et_al")

• Read the SoptSC article in NAR

• SoptSC is also available as a MATLAB package here

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.