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Published October 20, 2024 | Version v2
Dataset Open

Supplementary data for ENACT: End-to-End Analysis and Cell Type Annotation for Visium High Definition (HD) Slides

Creators

  • 1. ROR icon Sanofi (Canada)
  • 2. ROR icon Sanofi (Spain)
  • 3. Sanofi (USA)
  • 4. ROR icon Sanofi (France)

Description

This project contains the datasets used to evaluate and reproduce the results of ENACT (End-to-End Analysis and Cell Type
Annotation for Visium HD Slides). The dataset consists of:

  • a sample Visium HD sample of human colorectal cancer, courtesy of 10X Genomics (Visium HD Spatial Gene Expression Library, Human Colorectal Cancer (FFPE) - 10x Genomics). All credit goes to 10X Genomics.
  • configuration files to be used to reproduce the results provided in the ENACT publication, 
  • evaluation plots used in the ENACT publication, and
  • results obtained after running ENACT on the human colorectal cancer sample using the four bin-to-cell assignment methods (naive, weighted_by_area, weighted_by_transcript, and weighted_by_cluster) and the three cell annotation methods (Sargent, CellAssign, CellTypist)

Additionally, results from running ENACT on the following three public VisiumHD samples are provided to showcase ENACT’s tissue-agnostic nature:

 

Files

ENACT_additional_samples.zip

Files (18.4 GB)

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md5:8e99cee82b74419cf289374d815f172f
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md5:e2431ce056ab9a6bdb27db025d1d454a
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Additional details

Dates

Updated
2024-10

Software

Repository URL
https://github.com/Sanofi-Public/enact-pipeline
Programming language
Python
Development Status
Active

References