xpore 2.2

xPore is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing.

Installation

xPore requires Python3. To install the latest release with PyPI (recommended), run

$ pip install xpore 

Documentation

Please refer to our xPore documentation (https://xpore.readthedocs.io) for additional information, a quick start guide, and details on the data processing and output file format.

xPore is described in details in Pratanwanich et al. Nat Biotechnol (2021)

Release History

The current release is xPore v2.2, which adds support for genome-aligned eventalign output (via the new --kmer_source model_kmer flag) and RNA004 data (now the default xpore-diffmod prior).

Please refer to the github release history for previous releases: https://github.com/GoekeLab/xpore/releases

Citing xPore

If you use xPore in your research, please cite

Ploy N. Pratanwanich, et al. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nat Biotechnol (2021), https://doi.org/10.1038/s41587-021-00949-w.

Getting Help

We appreciate your feedback and questions! You can report any error or suggestion related to xPore as an issue on github. If you have questions related to the manuscript, data, or any general comment or suggestion please use the Discussions.

Contribution

We appreciate contributions on bug fixes and potential new features. Please read our Contribution Guidelines for more information.

Thank you!

Contact

xPore is maintained by Ploy N. Pratanwanich, Yuk Kei Wan and Jonathan Goeke from the Genome Institute of Singapore, A*STAR.