The latest stable version is V2.9.6.
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
conda create -n cxg python=3.9
conda activate cxg
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
https://www.biorxiv.org/content/10.1101/2023.07.11.548639v1
More tutorial slides for multi-omics datasets (RNA, ATAC, CITE-seq, spatial transcriptomics) are coming soon (Q1/Q2 2024).