excellxgene 2.3.8

Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.

Exploratory CellxGene (ExCellxGene)

Video vignettes to come!

Installation

1. 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

2. 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

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

4. 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

5. 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!