"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.
Clone the project repository and create a new conda environment if needed. Then, from the top directory of the project, run pip install --editable .
The dependency on graph-tool currently requires a separate installation step. Run conda install -c conda-forge graph-tool.
Bone proteogenomics analysis (GitHub)
Generate SQLite databases for the list of full-length isoforms derived from the LRP pipeline.
This includes two sets of GTF annotation files: 1. Full-length isoforms with ORFs that align to Leafcutter junction cluster 2. Full-length isoforms with ORFs that do not align to Leafcutter junction cluster
Link to processed data can be found in here.
Conducted ORF-related analysis to identify sQTLs that affect full-length isoforms that potentially undergo nonsense mediated decay (NMD) and may result in new expression.