sgosline/reshape-immune-output repository overview

⁠scRNA-seq Immune Annotation

This directory stores workflows that tie specific immune annotation tools to existing data and then stores the results in a Synapse table⁠.These workflows will take data in a single format and run various immune annotation tools on them and harmonize the results.

⁠Tools available

Current tools supported.

• ImmClassifer: this is currently supported
• Garnett: this is under development
• Moana: this has not been started yet.

⁠Files compared

What datasets can be used to run these on? Currently waiting on annotations to be complete.

⁠Results

We plan to save results in a Synapse table⁠ to then carry out analysis on them. Questions we hope to ask include (but are not limited to):

• What immune types are showing up in which tumor types?
• What is the fraction of unannotated cells?
• Which methods agree the most? ...