Example notebooks

Data preparation

• Standard pipeline for scooby: analyzing 10K Multiome PBMC dataset from 10X genomics
  • Introduction
  • Import library and environment setup
  • Read count matrix
  • Read RNA Sequencing Data
  • Read ATAC Sequencing data
  • Save snapatac anndatas
  • Load multiple samples into snapatac
  • Create embedding
  • Create pseudobulk files for evaluation
• Scooby Evaluator
  • General Imports
  • scooby
  • Eval on Val