https://github.com/mkarikom/RSoptSC

Cell-cell communication and lineage inference for scRNA-seq data
https://github.com/mkarikom/RSoptSC

Last synced: 4 months ago
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Cell-cell communication and lineage inference for scRNA-seq data

• Host: GitHub
• URL: https://github.com/mkarikom/RSoptSC
• Owner: mkarikom
• License: other
• Created: 2018-08-30T15:51:23.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-05-03T11:38:50.000Z (about 1 year ago)
• Last Synced: 2024-01-14T19:43:21.111Z (5 months ago)
• Language: R
• Homepage: https://mkarikom.github.io/RSoptSC/
• Size: 137 MB
• Stars: 21
• Watchers: 4
• Forks: 10
• Open Issues: 8
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Lists

• awesome-cell-cell-communication - RSoptSC - [R]- RSoptSC enables cell-cell communication and lineage inference for scRNA-seq data. (Uncategorized / Uncategorized)

README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/"

)

```

# RSoptSC 

[![Build Status](https://travis-ci.com/mkarikom/RSoptSC.svg?branch=master)](https://travis-ci.com/mkarikom/RSoptSC)

## Updates

* Demo SoptSC at [`vignette("Joost_et_al")`](https://mkarikom.github.io/RSoptSC/articles/Joost_et_al.html)

* Read the SoptSC article in [NAR](https://doi.org/10.1093/nar/gkz204)

* SoptSC is also available as a MATLAB package [here](https://github.com/wangshuxiong/soptsc)

## Installation

```{r, eval = FALSE, echo = TRUE}

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](https://mkarikom.github.io/RSoptSC).