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 ananndata
object to perform downstream analysis provided byscanpy
. It provides many options for constructing the finalanndata
object by combining the count matrices representing difference splicing statuses differently. - Moreover,
pyroe
provides the interface for thequantaf
project, which is a database containing the quantification results of many publicly available datasets.
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)
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.