README.Rmd

---
title: "scINSIGHT for interpreting single cell gene expression in biologically heterogeneous data"
author: "Kun Qian, Wei Vivian Li"

date: "`r Sys.Date()`"
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

<img src="https://github.com/Vivianstats/data-pkg/raw/main/img/scINSIGHT.png" height="200" align="right" />

## Latest News

> 2022/05/19:

 + Version 0.1.4 released!

 
## Introduction

scINSIGHT uses a novel matrix factorization model to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. It assumes that each gene module is a sparse and non-negative linear combination of genes, and each cell is jointly defined by the expression of common and condition-specific modules.  Given multiple gene expression samples from different biological conditions, scINSIGHT aims to simultaneously identify common and condition-specific gene modules and quantify their expression levels in each sample in a lower-dimensional space.

Any suggestions on the package are welcome! For technical problems, please report to [Issues](https://github.com/Vivianstats/scINSIGHT/issues). For suggestions and comments on the method, please contact Kun (<kun_qian@foxmail.com>) or Vivian (<vivian.li@rutgers.edu>). 

## Installation

You can install `scINSIGHT` from [CRAN](https://cran.r-project.org/web/packages/scINSIGHT/index.html) with:

```{r gh-installation, eval = FALSE}
install.packages("scINSIGHT")
```

## Usage
Please refer to the [package vignette](https://github.com/Vivianstats/scINSIGHT/wiki/scINSIGHT-vignette) for examples about how to use the package functions.