SPLISOSM - Spatial Isoform Statistical Modeling

SPLISOSM (SPatiaL ISOform Statistical Modeling) is a Python package for analyzing RNA isoform patterns in spatial transcriptomics (ST) data. It employs multivariate kernel association tests to detect (i) spatial variability in isoform usage across spatial locations, and (ii) differential association between isoform usage and spatial covariates such as region annotation and RNA binding protein (RBP) expression.

Documentation

https://splisosm.readthedocs.io/

The documentation is under active development. Please check back later for more tutorials and end-to-end analysis examples using public long-read and short-read datasets.

Installation

Via GitHub (latest version):

pip install git+https://github.com/JiayuSuPKU/SPLISOSM.git#egg=splisosm

Via PyPI (stable version):

pip install splisosm

Citation

Su, Jiayu, et al. "Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM." Nature Biotechnology (2026): 1-12. link to paper