This repository comprises code and analyses for the Human Retina Cell Atlas (HRCA) project within the HCA framework, emphasizing the Eye Biological Network.
The main code can be found in the analysis directory of this repository. The subdirectories are organized according to the main figures corresponding to the manuscript. Each figure folder contains a document file that explains the running script, input, and output files. The utility folder comprises standalone scripts that have been used in multiple places. Additionally, two other repositories -- the preprocessing pipeline and benchmark scripts -- have also been developed and utilized in the HRCA.
Please refer to HRCA with scArches for a brief tutorial on training the reference model for HRCA v1.0 and performing label transfer using the trained reference model with scArches.
The HRCA v1.0 reference model with scArches is available for download on Zenodo at https://doi.org/10.5281/zenodo.14014720.
HRCA can be accessed through several interactive web browsers, including:
The HRCA paper: Li et al., bioRxiv 2023.
If you have any questions, please submit an issue to this repository.