https://github.com/tleonardi/nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://github.com/tleonardi/nanocompore

bioinformatics nanopore rna-modifications

Last synced: about 2 months ago
JSON representation

RNA modifications detection from Nanopore dRNA-Seq data

• Host: GitHub
• URL: https://github.com/tleonardi/nanocompore
• Owner: tleonardi
• License: gpl-3.0
• Created: 2018-08-05T10:43:07.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-01-22T15:46:45.000Z (5 months ago)
• Last Synced: 2024-04-26T19:04:05.954Z (2 months ago)
• Topics: bioinformatics, nanopore, rna-modifications
• Language: Python
• Homepage: https://nanocompore.rna.rocks
• Size: 138 MB
• Stars: 74
• Watchers: 10
• Forks: 11
• Open Issues: 30
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Codeowners: .github/CODEOWNERS

Lists

• awesome-nanopore - nanocompore - [Python] - [RNA modifications detection by comparative Nanopore direct RNA sequencing](https://www.biorxiv.org/content/10.1101/843136v1). (Software packages / RNA modification analysis)

README

        
![Nanocompore](docs/pictures/Nanocompore_logo.png)

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[![GitHub license](https://img.shields.io/github/license/tleonardi/nanocompore)](https://github.com/tleonardi/nanocompore/blob/master/LICENSE)

[![Python](https://img.shields.io/badge/Python-%3E%3D3.6-yellow)](https://www.python.org/)

[![BioRxiv](https://img.shields.io/badge/BioRxiv-10.1101%2F843136%20-red)](https://www.biorxiv.org/content/10.1101/843136v1.full)

[![PyPI version](https://badge.fury.io/py/nanocompore.svg)](https://badge.fury.io/py/nanocompore)

[![Downloads](https://pepy.tech/badge/nanocompore)](https://pepy.tech/project/nanocompore)

[![Build Status](https://travis-ci.com/tleonardi/nanocompore.svg?token=2uTrW9fP9RypfMALjksc&branch=master)](https://travis-ci.com/tleonardi/nanocompore)

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**Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples**

Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.

**Full documentation is available at http://nanocompore.rna.rocks**

[![Nanocompore](docs/pictures/worflow.png)](http://nanocompore.rna.rocks)

## Companion repositories

* [NanoCompore_pipeline](https://github.com/tleonardi/nanocompore_pipeline): Nextflow pipeline to preprocess data for NanoCompore

* [Nanocompore_analysis](https://github.com/tleonardi/nanocompore_paper_analyses): Analyses performed with Nanocompore for the BioRxiv preprint

* [NanopolishComp](https://github.com/tleonardi/NanopolishComp): Collapse Nanopolish eventalign output per kmer, required before running NanoCompore

## Main authors

* Tommaso Leonardi - tom {at} tleo.io

* Adrien Leger - aleg {at} ebi.ac.uk