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run-cellxgene.md

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cellxgene

install dependencies

(pip)pip3 install scanpy --upgrade

(pip)pip3 install anndata --upgrade

install

(pip)pip3 install cellxgene --upgrade --user

run

cellxgene launch [path-to-your-object/name-object.h5ad] --experimental-annotations-ontology --experimental-enable-reembedding --open

notes

  • follow inside () for ubuntu

tricks for macOS

  1. to open terminal go to spotlight (magnifying glass symbol on the very top right corner) and type terminal
  2. if you don't know your file path, get a finder window right next to the terminal window. Select the h5ad file in finder and drag it to terminal