Branching topology of the human embryo transcriptome revealed by entropy sort feature weighting
Description
This repository stores the data and code used to generate the human pre-implantation embryo results in our publication titled, "Branching topology of the human embryo transcriptome revealed by entropy sort feature weighting". The data is subset into two sub folders whose recommended order of usage is as follows: 1. Human_Embryo_Analysis - Contains the code used to generate all early human embryo scRNA-seq results in our publication. Python files with the the suffix, "_Workflow.py" contain the code required to reproduce results and plots. 2. Synthetic_Data - Contains the code used to generate all Dyngen synthetic scRNA-seq dataset results in our publication. Python files with the the suffix, "_Workflow.py" contain the code required to reproduce results and plots. We would like to highlight that we have provided exact copies of the early human embryo scRNA-seq counts matrices used in the paper to make our work as accessible as possible. However, we recommend that researchers who wish to use the datasets we used in their own work start from the source data (e.g. the Gene Expression Omnibus repositories) to maintain their integrity. Details of each dataset used for this work are provided in the experimental procedures section of our manuscript.
Files
Steps to reproduce
Python files with the the suffix, "_Workflow.py" contain the code required to reproduce results and plot. Relevant Github repositories for accessing code and workflows are: https://github.com/aradley/cESFW?tab=readme-ov-file https://github.com/aradley/cESFW_Embryo_Topology_Paper/tree/main