• Pixie adds conda environments in project directories.
• Docker/Singularity
• Conda
• Just document dependencies

Kegg to GREAT

https://maayanlab.cloud/Enrichr/help#background&q=4

• Link above shows how to calculate odds ratio
• Use fold enrichment instead of odds ratio
• Look in code for fold enrichment, but suspicion is that fold enrichment is pre-log changed

probability over background = odds ratio

– Diego

• Odds ratio looks like fisher test

Lee

Comparing loops between conditions is not a solved problem

– Matt

The best way would be to have replicates of each conditions, which requires deep sequencing

– Lee

Diego

• Going through the CisBP table
• Can't find data

• Uniprob contains lots of data

• We want real data, not peaks

  – Matt

Phil

• Still thinking about DNA corp
• Nothing else to talk about

Xioting

• Put together LLMs to run on cluster
• Struggling to put together Docker container
• GPU run failures