Welcome to the documentation for pyroe

What is pyroe?

The pyroe package provides useful functions for analyzing single-cell or single-nucleus RNA-sequencing data using alevin-fry.

Contents:

• Installing pyroe
• Preparing an expanded transcriptome reference for quantification with alevin-fry
  • Preparing a spliced+intronic transcriptome reference
  • Preparing a spliced+unspliced transcriptome reference
  • Notes on the input gene annotation GTF files for building an expanded reference
• Processing alevin-fry quantification result
• load_fry() full Usage
  • Required Parameters
  • Optional Parameters
  • load_fry Notes
  • Returns
• Fetching and loading preprocessed quantification results
  • fetch-quant full usage
  • The ProcessedQuant class
• Generating a gene id to gene name mapping
  • id-to-name full usage
• Converting quantification results
  • convert command full usage
• License

Indices and tables

• Index

• Module Index

• Search Page