TabulaSapiens

This repository holds code to analyze data from the Tabula Sapiens v2.0 dataset. The analysis is focused on transcription factors.

Contents

Identification of transcription factor programs:

• based on correlation:
  • cosine
  • spearman
• with dimensionality reduction:
  • pca + spearman
• cNMF: https://github.com/dylkot/cNMF

Prediction of transcription factor binding sites:

• retrieval of transcription factor binding motifs from JASPAR: https://jaspar.elixir.no/
• retrieval of corresponding amino acid sequences
• fine-tuned custom esm2 model