pyroe

The main purpose of pyroe is to provide the python interface for loading the quantification results of single-cell sequencing data generated by alevin-fry and simpleaf.

• The major function of pyroe is the load_fry function, which loads the quantification results into an anndata object to perform downstream analysis provided by scanpy. It provides many options for constructing the final anndata object by combining the count matrices representing difference splicing statuses differently.
• Moreover, pyroe provides the interface for the quantaf project, which is a database containing the quantification results of many publicly available datasets.

Background

Alevin-fry is a fast, accurate, and memory frugal quantification tool for preprocessing single-cell RNA-sequencing data. Detailed information can be found in the alevin-fry pre-print, and paper.

simpleaf provides a simple and easy-to-use interface for running alevin-fry, and also more advanced features such as designing and executing custom workflows for single-cell data analysis. (Paper and Documentation)

Major Updates

Since Pyroe v0.10.0, the functionality for creating augmented transcriptome references and generating gene ID to gene name file has been moved to the roers packge, which is automatically installed together with simpleaf. For all our users, we recommend using the simplified command line interface provided in simpleaf to process your single-cell sequencing data. The simpleaf index command will automatically generate the augmented transcriptome reference (including the gene ID to gene name file), indexing the reference for you.