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scExplorer
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scExplorer
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# Single Cell Explorer (ver 1.1.0) Thank you for visiting wiki of Single Cell Explorer. Singel Cell Explorer is available open-source under the GNU LGPLv3 license. This web application only run on Linux. Authors: Di Feng, Dechao Shan Contact: di_feng@yahoo.com ### Site URL: ##### http://singlecellexplorer.org ##### http:18.204.165.197 ### Source code, database files, python scripts for Jupyter notebook http://18.204.165.197/download.html ### Jupyter Notebook walkthrough http://18.204.165.197/analysis.html ### Installation guide http://18.204.165.197/install.html ### Installation of Single Cell Explorer from Source ##### quickest way: run setup shell scripts from http://18.204.165.197/downloads/setupSCexplorer.sh ### From console (step by step) #### Update (based on ubuntu 18.04 or 16.04) ###### sudo apt-get update ###### sudo apt-get install -y build-essential ###### sudo apt-get install -y ssh libssl-dev libffi-dev libxml2-dev libxslt1-dev zlib1g-dev zip unzip libfftw3-dev libcurl3 openssl #### Install python3 ###### sudo apt-get install -y python3 python3-pip python3-dev #### Install MongoDB, create database paths, and start MongoDB server ###### cd ~ ###### mkdir -p mongodb ###### cd mongodb ###### wget https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-ubuntu1604-4.0.10.tgz ###### tar -zxvf mongodb-linux-x86_64-ubuntu1604-4.0.10.tgz ###### mkdir scdb ###### mkdir log ###### sudo ./mongodb-linux-x86_64-ubuntu1604-4.0.10/bin/mongod --dbpath "./scdb" --port 27017 --wiredTigerCacheSizeGB 1 --fork --logpath "./log/scdb.log" #### Load database schema & sample data into MongoDB ###### cd ~/mongodb/ ###### wget http://18.204.165.197/downloads/scDB.zip ###### unzip scDB.zip ###### mkdir dumpfiles ###### mv scDB dumpfiles ###### mongodb-linux-x86_64-ubuntu1604-4.0.10/bin/mongorestore dumpfiles #### Launch Single Cell Explorer web application ###### sudo pip3 install --upgrade pip ###### sudo pip3 install numpy gunicorn pymongo sklearn pandas django==2.2 torchvision ###### cd ~ ###### mkdir singleCell ###### cd singleCell ###### wget http://18.204.165.197/downloads/singleCellExplorer.zip ###### unzip singleCellExplorer.zip ###### cd singleCellExplorer ###### python3 manage.py runserver 0.0.0.0:8000 # usage --For Data registration: The following items are mandatory. study: The name of the study, which should include all the samples as a collection. species: Human, Mouse, etc tissue: The biological source of the samples (blood, inflamed, uninvolved etc). mapType: Currently, we support tsne, umap, and phate. name: The map name will be used in the single cell explorer map viewer. The following information is optional, but we encourage you to use. disease: This help to create a collected atlas of normal tissue or disease tissue. source: You can use internal or external to distinguish the data source. author: This indicate the contact person of the data or author who created the map in single cell explorer. subjectid: Subject ID, which represent the each donor in the study, should be unique. Sometime, there are multiple tissue samples could be collected from the same individual or subject ID. Usage: For a study that collect blood, uninvolved, and involved samples from multiple subjects. We can create the following dictionary. You can also add more meta information in the dictionary. mapinfo={ “study”:”Disease Collection”, “species”: “Homo sapien”, “tissue”: “involved”, “mapType”:”tsne”, “name”:”involved sample”, “source”:”public data”, “author”:”Me”, “subjectid”:”CT0001”, “comment”:”” } --Multiple Sample Comparison Once you registered all the samples from a study. You can cross-compare gene expression among multiple donor/subjects within that study. You can select 1) the study 2) the right tissue to compare, 3) the cell type 4) the gene of interest for comparison.
