Here is the code repository of the analysis for the joint Australia Society of Immunology / Oz Single Cell Hackathon

There are three immunologists top challenges included in this Hackathon:

1. Minimal cluster identification/marker extraction: Identifying the ideal/minimal (i.e. 12-15) protein marker combinations to identify the maximal number of cell clusters based on RNA ± CITE-seq reference data set.
   • 1a Novel pipeline that allows extraction
   • 1b Utility: Lead to better panel choice for subsequent experiments
   • 1c Reference of rank order gene-protein correlation values (e.g. CD8 terrible with RNA, great with protein)
   • 1d Create minimal marker reference from dataset that can evolve for people to split into all immune subsets. Ala Simon Haas but better? Different?
   • 1e Novel biomarker identification from clinical cohorts
2. Cell-cell, protein-protein interaction (visualisation? More refined? Interpretation?)
   • 2a Don’t reinvent the great databases out there? Rather leverage these so immunologists can better use them
   • 3b Interfacing with the proteogenomics data
3. Can we use RNA+protein references to inform genes likely to be expressed in FACS subsets? Vice versa?
   • 3a Hopefully have a normalised reference FACS whole blood data set. Perhaps healthy vs COVID

I'll post the analysis pipeline specifically for the challenge #1 and #2 in /main folder

The /data folder contains the data download instructions

The /src folder contains the necessary R functions and other relevant files

The /job folder contains the qsub script for HPC jobs including the stderr and stdout files