Week Nine | Testing weights for module stability

Tasks

1. Testing weights for module stability Status: In progress Branch: None PR: None

2. Initiate (third) PR for netboxr ToolShed upload Status: Complete Branch: None PR: None

3. Fix issues with netboxr tests Status: In progress Branch: None PR: None

4. Initiate PR with parent repository to merge netboxr updates Status: In progress Branch: None PR: None

5. Meeting with supervisors Status: Thursday Branch: None PR: None

Progress report

netbox2010, ebc, no weights

netbox2010, ebc, weights

netbox2010, lec, no weights

netbox2010, lec, weights

netbox2010, Louvain, no weights

netbox2010, Louvain, weights

netbox2010, Leiden, no weights

netbox2010, Leiden, weights

pathway_commons_v8_reactome, ebc, no weights

pathway_commons_v8_reactome, ebc, weights

pathway_commons_v8_reactome, lec, no weights

pathway_commons_v8_reactome, lec, weights

pathway_commons_v8_reactome, Louvain, no weights

pathway_commons_v8_reactome, Louvain, weights

pathway_commons_v8_reactome, Leiden, no weights

pathway_commons_v8_reactome, Leiden, weights

I made changes to the netboxr Galaxy tool based on feedback from the last PR, including XML file formatting, error detection, adding categories as well as a longer description to the .shed.yml file, and others (commit - I accidentally commited the .Rproject and .Rhistory files as well, but deleted them later on.). Following this, I initiated another (and hopefully final) PR.

Remaining tasks for Galaxy tool development (list not exhaustive):

• Adding missing parameters (resolution, weights, etc.)
• Adding Pathway Commons network
• Adding option for users to upload their own network
• Improving help section (XML tool)