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https://github.com/GoekeLab/xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing
https://github.com/GoekeLab/xpore
genomics machine-learning modification nanopore nanopore-sequencing python rna rna-modifications rna-seq transcriptomics
Last synced: about 2 months ago
JSON representation
Identification of differential RNA modifications from nanopore direct RNA sequencing
- Host: GitHub
- URL: https://github.com/GoekeLab/xpore
- Owner: GoekeLab
- License: mit
- Created: 2020-01-06T07:44:22.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-04-29T04:16:52.000Z (2 months ago)
- Last Synced: 2024-04-29T05:26:26.121Z (2 months ago)
- Topics: genomics, machine-learning, modification, nanopore, nanopore-sequencing, python, rna, rna-modifications, rna-seq, transcriptomics
- Language: Python
- Homepage: https://xpore.readthedocs.io/
- Size: 4.96 MB
- Stars: 127
- Watchers: 9
- Forks: 22
- Open Issues: 27
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Lists
- awesome-nanopore - xPore - [Python] - [Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore](https://doi.org/10.1038/s41587-021-00949-w). (Software packages / RNA modification analysis)
README
[](https://badge.fury.io/py/xpore)
[](https://xpore.readthedocs.io/en/latest/?badge=latest)
[](https://pepy.tech/project/xpore)
---
xPore is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing.
### Installation
xPore requires [Python3](https://www.python.org).
To install the latest release with PyPI (recommended), run
```sh
$ pip install xpore
```
---
### Documentation
Please refer to our xPore documentation ([https://xpore.readthedocs.io](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)](https://doi.org/10.1038/s41587-021-00949-w)
---
### Release History
The current release is xPore v2.1.
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](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](https://github.com/GoekeLab/xpore/issues). If you have questions related to the manuscript, data, or any general comment or suggestion please use the [Discussions](https://github.com/GoekeLab/xpore/discussions).
---
### Contribution
We appreciate contributions on bug fixes and potential new features. Please read our [Contribution Guidelines](https://github.com/GoekeLab/xpore/blob/master/CONTRIBUTING.md) for more information.
Thank you!
---
### Contact
xPore is maintained by [Ploy N. Pratanwanich](https://github.com/ploy-np), [Yuk Kei Wan](https://github.com/yuukiiwa) and [Jonathan Goeke](https://github.com/jonathangoeke) from the Genome Institute of Singapore, A\*STAR.