scINSIGHT for interpreting single cell gene expression in biologically
heterogeneous data
================
Kun Qian, Wei Vivian Li
2025-10-19

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

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

## Latest News

> 2025/10/19:

-   Version 0.1.5 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/package=scINSIGHT/index.html)
with:

``` r
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.
