Seeking Guidance on Data Format (my own reaction and genes files from KEGG) Conversion for COMPASS Analysis #108
Description
Hello,
Firstly, I want to express my gratitude for developing such exceptional software. I am currently preparing to analyze my data with COMPASS and need some assistance on how to properly format my inputs for this process. My data consist of:
- Single-cell RNA sequencing (scRNA-seq) data.
- A CSV file with my own reaction modules. This file serves as an adjacency matrix representing the relationships between reactions and compounds, where the values 0, 1, and -1 indicate the type of relationship.
- A JSON file that lists the genes associated with each reaction.
Could anyone provide guidance or advice on how to convert my second and third inputs (the reaction modules CSV with 0, 1, -1 values and the genes JSON from KEGG) into a format compatible with COMPASS? Understanding how to perform this conversion is essential for leveraging the software to achieve my desired analytical outcomes.
Thank you immensely for any assistance or direction you can offer!