README.Rmd

---
output: github_document
---

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

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# scSpotlight <a href="https://obenno.github.io/scSpotlight/"><img src="man/figures/logo.png" align="right" height="139" alt="scSpotlight website" /></a>

<!-- badges: start -->
[![scSpotlight status badge](https://obenno.r-universe.dev/badges/scSpotlight)](https://obenno.r-universe.dev/scSpotlight)
<!-- badges: end -->

The goal of scSpotlight is to simplify your single cell analysis and easily
annotate your dataset with curated cell type markers. `scSpotlight` is built on
[shiny](https://shiny.posit.co/), [Seurat](https://satijalab.org/seurat/) 
and [regl-scatterplot](https://github.com/flekschas/regl-scatterplot). 
Please refer to the documentation website for detailed instructions:

- https://obenno.github.io/scSpotlight/
- https://scspotlight.netlify.app/ (EN, CN)
 

```{r, echo=FALSE, out.width="80%"}
knitr::include_graphics("https://raw.githubusercontent.com/obenno/scSpotlight/main/vignettes/articles/images/scSpotlight_landingFigure.png")
```

## Installation

You can install the development version of scSpotlight from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("obenno/scSpotlight")
```

or a much faster installation with `pak`:

``` r
# install.packages("pak")
pak::pkg_install("obenno/scSpotlight")
```

## Docker

To pull the latest image from the command line

```
docker pull registry-intl.cn-hangzhou.aliyuncs.com/thunderbio/scspotlight:0.0.3
```

To run the app on `port:8081`, please use the command below:

```
docker run -p 8081:8081 registry-intl.cn-hangzhou.aliyuncs.com/thunderbio/scspotlight:0.0.3 Rscript -e 'scSpotlight::run_app(options = list(port=8081, host="0.0.0.0", launch.browser = FALSE), runningMode="processing")'
```