This is the GitHub page for the "Single-cell transcriptome atlas of Drosophila gastrula 2.0" (Sakaguchi et al., 2023).
Processed data including UMI count tables, Seurat objects and loom files are available here.
Loom files are compatible with viewing in SCope.
Jupyter Notebooks used for data analysis are also available on this page.
The viewer, described below, allows browsing the dataset, including cluster information and gene expression level on UMAP, the gene expression level in each pair-rule stripe, and spatial gene expression reconstructed by Perler and NovoSpaRc on the browser.
The viewer environment is built using Docker, and the installation process is as follows.
If you have not yet installed Docker, install Docker desktop
Download "viewer.tar.gz" containing the Docker images of the viewer from here.
- Choose the arm64/amd64 flygastrula2_viewer.tar depending on your device, and move it to your home directory.
- Start Docker desktop.
- Start Terminal, move to the home directory, and load the image into Docker by the following command.
docker load -i flygastrula2_viewer.tar
- Make the container by the following command.
docker run -it -p 8050:8050 --name flygastrula2_viewer -w /home/ flygastrula2_viewer python app.py
- When the display shows "Dash is running on http://0.0.0.0:8050/",
access http://0.0.0.0:8050/ in your browser.
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For the browser, Chrome is recommended.
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Now, you can browse the Set3-CAP data, including
- Cluster information and gene expression level on UMAP (Seurat clusters, Sub-clusters, Genes)
- Gene expression level in each pair rule strip (Stripe)
- Spatial gene expression reconstructed by Perler and NovoSpaRc (VISH and Dual VISH)
- You can stop the Docker container with the following commands in Terminal.
Control + P + Q
docker stop flygastrula2_viewer
docker rm flygastrula2_viewer
- If you want to start again, please start from 4.