.. scATS documentation master file, created by sphinx-quickstart on Mon Jan 27 18:49:34 2025. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to scATS's documentation! ================================= **scATS** is a tool designed to **de novo** quantify alternative transcription start site (ATS) from paired-end 5'-end single-cell RNA sequencing (scRNA-seq) data. It achieves this by modeling the decreasing trend of short-read counts in exons from the 3' to the 5' ends of transcripts, which is attributable to **RNA degradation**. **scATS** introduces two novel metrics (`α` and `β`) to precisely quantify RNA degradation, and provides both raw (`ψ`) and corrected (`θ`) metrics to correct ATS expression profiles from resulting distortions. .. image:: _static/method.png :alt: scATS Workflow Diagram :align: center :scale: 40% Users are required to specify the genes and cells to be included in the analysis, as well as the minimum number for each gene. With these parameters, **scATS** can accurately calculate the expected abundance of ATS isoforms and conduct differential analysis for specific groups. To use scATS, you can follow the instructions below: .. toctree:: :caption: Contents: :maxdepth: 2 md/Installation md/Usage md/Disease model md/Getting Help md/Citing scATS Citing scATS ------------ If you use scATS in your research, please cite ********************************** Contacts -------- scATS is developed and maintained by `Zijie Xu `_ and `Chao Tang `_ from Sichuan University. If you want to contribute or have any questions, please leave an issue in our `repository `_. Thank you !