Pan-GI Cell Atlas

• Full healthy reference	adult/paediatricfile_download	embryo/fetalfile_download
  Healthy reference by organ (adult/paediatric)	Oral cavityfile_download	Oesophagusfile_download	Stomachfile_download	Small intestinefile_download	Large intestinefile_download

• Dataset Name	Interactive Viewer	H5AD Data	RDS Data
  Healthy reference	pageview	file_download	file_download
  Extended	pageview	file_download
  Extended+	pageview	file_download

• chevron_rightLineages

  Dataset Name	Interactive Viewer	H5AD Data	RDS Data	H5AD extended	RDS extended
  T and NK cells	pageview	file_download	file_download	file_download	file_download
  B and B plasma cells	pageview	file_download	file_download	file_download	file_download
  Myeloid cells	pageview	file_download	file_download	file_download	file_download
  Endothelial cells	pageview	file_download	file_download	file_download	file_download
  Neural cells	pageview	file_download	file_download	file_download	file_download

  • chevron_rightMesenchymal cells (by age)

    Dataset Name	Interactive Viewer	H5AD Data	RDS Data	H5AD extended	RDS extended
    Mesenchymal (adult/pediatric)	pageview	file_download	file_download	file_download	file_download
    Mesenchymal (first trimester)	pageview	file_download	file_download
    Mesenchymal (second trimester)	pageview	file_download	file_download

  • chevron_rightEpithelial cells (by region/age)

    Dataset Name	Interactive Viewer	H5AD Data	RDS Data	H5AD extended	RDS extended
    Oral mucosa	pageview	file_download	file_download
    Salivary gland	pageview	file_download	file_download
    Oesophagus	pageview	file_download	file_download
    Stomach	pageview	file_download	file_download	file_download	file_download
    Small intestine (adult/pediatric)	pageview	file_download	file_download	file_download	file_download
    Small intestine (first trimester)	pageview	file_download	file_download
    Small intestine (second trimester)	pageview	file_download	file_download
    Large intestine (adult/pediatric)	pageview	file_download	file_download	file_download	file_download
    Large intestine (first trimester)	pageview	file_download	file_download
    Large intestine (second trimester)	pageview	file_download	file_download

• chevron_rightDownload all
  file_downloadObjects file_downloadModels

  codeDownload using terminal

  Download all of the objects:

  content_copy

  wget https://cellgeni.cog.sanger.ac.uk/gutcellatlas/pangi/objects_pangi_20251029.zip

  Download all of the models (kNN and scANVI models):

  content_copy

  wget https://cellgeni.cog.sanger.ac.uk/gutcellatlas/pangi/models_pangi_20251029.zip

  Close

• chevron_rightRelease notes
  • Version 20251029
    • - Fixed bugs in metadata
    • - Updated interactive viewer links with the links from CELLxGENE Discover collection
    • - Added a yml file of conda environment for scvi to models.zip
  • Version 20241119
    • - First version, published atlas

Any questions? Please submit an issue in our GitHub repository