Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.
Project description
Exploratory CellxGene (ExCellxGene)
Video vignettes to come!
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 (we need to install the TBB threading layer as well):
conda create -n cxg python=3.8
conda activate cxg
conda install tbb=2020.3 tbb-devel=2020.3
- Install excellxgene with pip:
pip install excellxgene
If your operating system is CentOS, then you may run into issues installing dependencies that require up-to-date gcc or g++ compilers. Please install with the following and try reinstalling excellxgene with pip:
conda install -c conda-forge gcc cxx-compiler
- 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/excellxgene
cd excellxgene
Datasets are stored in example-dataset
- Launch excellxgene with:
excellxgene launch example-dataset
This should launch an excellxgene session with all the datasets in example-datasets/ loaded in.
If you're running excellxgene remotely, please launch with:
excellxgene launch example-datasets --host 0.0.0.0
Ping me on the Biohub slack (@Alec) if you have any questions!
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excellxgene-2.3.8.tar.gz
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