tidesurf documentation

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Python 3.10 Python 3.11 Python 3.12 Python 3.13 License: GPL v3 Code style: ruff Code coverage Python package PyPI - Version

tidesurf documentation#

tidesurf

This is the documentation for tidesurf, a Tool for IDentification and Enumeration of Spliced and Unspliced Read Fragments, implemented in Python. It enables the quantification of spliced and unspliced reads from 10x Genomics 5’ and 3’ scRNA-seq data, using the 10x Genomics Cell Ranger output.

Note

This project and its documentation are under active development.

Note

In the future, we aim to support other single-cell RNA-seq data formats, such as Smart-seq2.

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Citation#

If you use tidesurf in your research, please cite the following publication:

Schleicher, J.T., Klingler, D., and Claassen, M. (2026). Accurate quantification of spliced and unspliced transcripts for single-cell RNA sequencing with tidesurf. PLoS One 21(8): e0355867; DOI: 10.1371/journal.pone.0355867.

@article{10.1371/journal.pone.0355867,
   doi = {10.1371/journal.pone.0355867},
   author = {Schleicher, Jan T. AND Klingler, Doreen AND Claassen, Manfred},
   journal = {PLOS ONE},
   publisher = {Public Library of Science},
   title = {Accurate quantification of spliced and unspliced transcripts for single-cell RNA sequencing with tidesurf},
   year = {2026},
   month = {08},
   volume = {21},
   url = {https://doi.org/10.1371/journal.pone.0355867},
   pages = {1-23},
   number = {8},
}
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