README.Rmd

---
title: "scLink: Inferring gene networks from single-cell gene expression data"
author: "Wei Vivian Li"

date: "`r Sys.Date()`"
output: github_document
self_contained: no
---

<!-- 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/scLink/raw/master/inst/docs/sclink.png" height="300" align="right" />


```{r echo=FALSE, results="hide", message=FALSE}
library("badger")
```

```{r, echo = FALSE, results='asis'}
cat(
	badge_cran_release("scLink", "green")
	# badge_cran_download("scLink", "grand-total", "green")
)
```



Introduction
------------

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

You can also browse scLink's applications and results at its [web app](https://rutgersbiostat.shinyapps.io/sclink/).

Installation
------------

The package is available on CRAN. For installation please use the following codes in `R`
``` r
install.packages("scLink")
```


Quick start
-----------

`scLink` has three main functions:

-   `sclink_norm` for pre-processing gene expression data
-   `sclink_cor` for calculating the co-expression matrix by scLink
-   `sclink_net` for constructing the gene co-expression network by scLink

For detailed usage, please refer to the package [manual](https://github.com/Vivianstats/scLink/blob/master/inst/docs/) or [vignette](https://github.com/Vivianstats/scLink/blob/master/vignettes/).


Citation
-----------

Wei Vivian Li, Yanzeng Li. (2021) scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. Genomics, Proteomics & Bioinformatics, in press.
[Link](https://doi.org/10.1016/j.gpb.2020.11.006)