Exploratory CellxGene (ExCellxGene)

V2.9.6

The latest stable version is V2.9.6.

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:

conda create -n cxg python=3.9
conda activate cxg

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

Preprint on how to do manual cell-type annotation using interactive tools:

https://www.biorxiv.org/content/10.1101/2023.07.11.548639v1

Tutorial slides highligting some use cases:

https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_8__Multimodal%20Annotations

More tutorial slides for multi-omics datasets (RNA, ATAC, CITE-seq, spatial transcriptomics) are coming soon (Q1/Q2 2024).