Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.
Project description
Exploratory CellxGene (ExCellxGene)
This fork implements some of the key features that have been highly requested by the data science team at CZBiohub.
Features include:
- Hotkeys (SHIFT+? to see a tooltip describing all available hotkeys)
- End-to-end interactive analysis and reembedding, with new embeddings hierarchically organized.
- LIDAR graph interaction mode (the airplane) - Show an interactive tooltip describing the cells underneath your cursor. Very helpful for the color impaired or for large datasets with hundreds of labels.
- Sankey plots
- Leiden clustering
- Label fusion and deletion
- Interactive selection of data layer for expression visualization
- Many other quality-of-life improvements.
Installation
- Install miniconda if conda not available already:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
- Create and activate a new environment:
conda create -n cxg python=3.7
conda activate cxg
- Install excellxgene with pip (the latest version should be
1.1.7)
pip install excellxgene
- Download the git repository to get the example datasets (assumes git is available, if not install it with conda install -c anaconda git)
git clone https://github.com/czbiohub/cellxgene
cd cellxgene
Datasets are stored in example-dataset
- Launch cellxgene with:
cellxgene launch example-dataset
This should launch a cellxgene session with all the datasets in example-datasets/ loaded in.
If you're running excellxgene remotely, please launch with:
cellxgene launch example-datasets --host 0.0.0.0
Ping me on the Biohub slack (@Alec) if you have any questions!
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