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

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Project description

Exploratory CellxGene (ExCellxGene)

Video vignettes to come!

V2.6.1

In the latest version, the internal file system used by excellxgene has been restructured. As a result, you will need to migrate your data to the new version. The easiest way to do this is with the following:

  1. Create a new conda environment (same instructions as in the installation section).
  2. Pip install excellxgene==2.6.1
  3. Copy/Move your h5ad to a NEW LOCATION.
  4. Launch the new version of excellxgene using the moved/copied data.
  5. Upload the metadata/genesets/etc downloaded from the old version of excellxgene to the new version.

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
  1. 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
  1. 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
  1. 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

  1. 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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Release history Release notifications | RSS feed

2.9.6

2.9.5

2.9.4 yanked

2.9.2

2.9.1

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broken

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unstable

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unstable

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unstable

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unstable

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unstable

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memory leakage with ray

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This version

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premature release

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Sankey broken again

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Bug with scatter plots

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Windows pathing bug still present

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