SGS: An Integrative Browser for Collaborative Visualization of Single-cell and Spatial Multimodal Data 👋

🎉 SGS, a user-friendly ⚡, collaborative ⚡ and versatile ⚡ browser for visualizing single-cell and spatial multiomics data, including scRNA, spatial transcriptomics, scATAC, scMethylC, sc-eQTL etc. With advanced features for comparative visualization, multi-panel coordiniate view, abundant visualization functions and collaborative exploration, SGS empowers researchers to unlocking the novel insights from scMulti-omics data 🎉.

🚀 Document

Instructions, documentation, and tutorials can be found at: SGS Website

💻 File Format and Conversion

• SGS supports various data formats including Anndata, Mudata, and genome-mapped files (GFF, VCF, BED, Bigwig, HiC, Biginteract, Longrange, methylC, Gwas,).
• The SgsAnnData R package enables seamless data format conversion with analysis tools like Seurat, ArchR, Signac, and Giotto.
• SgsAnnData can be access by the following links: SgsAnnData gtihub

⚙️ Installation

Make Sure Docker is installed on your server SGS primarily utilizes Docker and Flutter technologies to achieve graphical one-click installation. SGS supports the following three deployment methods:

🎈🎈🎈 Quick Start (recommended）

The SGS browser consists of two main components: the SGS server and SGS client. Once you have downloaded and installed the SGS client, you need to deploy the SGS server for data visualization.

Please note that SGS server deployment currently only supports Linux and MacOS systems!

Client deployment tutorial: https://sgs.bioinfotoolkits.net/document/installation.html#deploy-a-new-sgs-server

Custom manual installation (optional)

Method1: Script Installation

# Download shell script
wget https://raw.githubusercontent.com/fanglu0411/sgs/main/script/deploy.sh deploy-sgs.sh
# or use curl
curl -fsSL https://raw.githubusercontent.com/fanglu0411/sgs/main/script/deploy.sh -o deploy-sgs.sh

# Change permission
chmod 777 deploy-sgs.sh
# Run install command
./deploy-sgs.sh DB_PORT=33061 API_PORT=6102 WEB_PORT=1080

Method 2: Manual Installation

Step1: Pull images

• sgs-mysql sgs database image
• sgs-api sgs api image
• sgs-web optional for web app

sudo docker pull lufang0411/sgs-mysql:latest &&
sudo docker pull lufang0411/sgs-api:latest &&
sudo docker pull leeoluo/sgs-web:latest

If the official docker hub is not available for you, pleas run command below.

sudo docker pull registry.bioinfotoolkits.net/lufang0411/sgs-mysql:latest &&
sudo docker pull registry.bioinfotoolkits.net/lufang0411/sgs-api:latest &&
sudo docker pull registry.bioinfotoolkits.net/leeoluo/sgs-web:latest

Step2: Prepare working directory

sgs_path=/data/docker/vol/sgs

mkdir -r ${sgs_path} && cd ${sgs_path}
mkdir sgs && mkdir api
sudo chmod 777 sgs && sudo chmod 777 api

Step3: Run docker container

3.1 Setup port params

DB_PORT=33061
API_PORT=6102
WEB_PORT=1080

3.2 Start sgs-mysql

docker run --privileged -d \
    --restart=always \
    -v "${sgs_path}/mysql:/var/lib/mysql" \
    --name sgs-mysql \
    -p ${DB_PORT}:3306 \
    -e  MYSQL_ROOT_PASSWORD=${MYSQL_PASSWORD} \
    lufang0411/sgs-mysql:latest

3.3 Start sgs-api

docker run -dit \
    --restart=always \
    --name sgs-api \
    -v "${sgs_path}/api:/home/sgs/data" \
    -p ${API_PORT}:6102 \
    -p 6122:22 \
    --link sgs-mysql \
    lufang0411/sgs-api:latest

3.4 Start sgs-web (option al if you use SGS client).

docker run -d \
    --restart=always \
    --name sgs-web \
    -p ${WEB_PORT}:80 \
    --link sgs-api \
    -e API_URL=sgs-api:${API_PORT} \
    leeoluo/sgs-web:latest

🌱 Reporting Issues

If you found an issue, please report it along with any relevant details to reproduce it. Thanks.

😊 Contact

• Yi Wang (yiwang28@swu.edu.cn)
• Fang Lu (lufang0411@sina.com)
• Yongjiang Luo (lyjiang126@yeah.net)
• Tingting Xia (xtt199239@163.com)
• Jiahe Sun (sunjiahe0502@email.swu.edu.cn)

🌹 Citiation

👉 License

SGS Copyright (c) 2024 Wang lab. All rights reserved. This software is distributed under the MIT License (MIT).