lsbnb/mysort_2022 repository overview

Before your Journey, please prepare your expression file in gene symbols (like AIM2, TCL1A..). If you have raw reads in hands, you may consider to generate the FPKM file via web interface in our galaxy docker, docexpress_fastqc⁠.

The demo site for this docker image also can be found at http://mysort.iis.sinica.edu.tw⁠.

We also have a previous version of mySort on galaxy/Docker with less functionality available at Galaxy_mySROT⁠.

⁠Installation

⁠Step 0. Install the Docker engine and start the daemon.

⁠Step 1. Pull down Galaxy Docker image from Docker Hub.

⁠Step 2. Run the Docker container and set port numbers for network accessibility.

⁠Step 3. Launch localhost with port 8080 in a browser. (http://127.0.0.1:8080⁠ or http://localhost:8080⁠)

⁠Step 4. Click the demo buttom on the website or run the built-in workflow with example dataset to have a testrun.

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⁠The workflow from Raw reads to deep analysis on immune cell composition for each sample or group

⁠Citation

1. Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu and Chung-Yen Lin. A gene profiling deconvolution approach to estimating immune cell composition from complex tissues. BMC Bioinformatics. 2018 May 8;19(Suppl 4):154. doi: 10.1186/s12859-018-2069-6.