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vlt Launches "reproduce": A New Tool Challenging the Limits of Package Provenance
vlt's new "reproduce" tool verifies npm packages against their source code, outperforming traditional provenance adoption in the JavaScript ecosystem.
Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.
The latest stable version is V2.9.6. The current version of exCellxgene relies on anndata==0.7.8, so might crash with anndata objects generated with anndata==0.8.0 or above. Until we fix this bug, we recommend users to follow the installation instruction below. The key part is installing exCellxgene, then upgrading the anndata version to 0.8.0 in the "cxg" conda environment.
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=3.8
conda activate cxg
pip install excellxgene
pip install anndata==0.8.0
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
git clone https://github.com/czbiohub/excellxgene
cd excellxgene
Datasets are stored in example-dataset
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).
FAQs
Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.
We found that excellxgene demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 4 open source maintainers collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
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