Code for cross-species and uTAR sequence homology analyses for two Tabula Microcebus papers

The Tabula Microcebus Consortium et al. Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism. bioRxiv 2021.12.12.469460 (2021) doi:10.1101/2021.12.12.469460 (biorxiv link)

The data behind this figure includes:

• Unifying cell types across human, mouse, and mouse lemur
• Subsetting scanpy objects to only shared cell types
• Subsetting scanpy objects on homologous genes
• Creating a single scanpy object of human, mouse, and mouse lemur
• Performing Xi (Xi = $\Xi$ Greek letter) correlation on bootstrapped trios of (human, mouse, mouse lemur) cells
• Plotting $\Delta\Xi$ correlations to compare human:lemur vs human:mouse

The Tabula Microcebus Consortium et al. Mouse lemur transcriptomic atlas elucidates primate genes, physiology, disease, and evolution. bioRxiv 2022.08.06.503035 (2022) doi:10.1101/2022.08.06.503035 (biorxiv link)

• nf-predictorthologs pipeline
  • Used orpheum to translate reads from unannotated transcriptionally active regions (uTARs)
    • Orpheum bisects reads into either coding or non-coding
  • Annotated translated protein sequences using DIAMOND
• Create Venn Diagram of overlap between region annotations