Metadata-Version: 2.1
Name: nanocompore
Version: 1.0.0rc3.post2
Summary: Software package that identifies raw signal changes between two conditions from https://github.com/jts/nanopolish resquiggled dRNA-Seq data.
Home-page: https://github.com/tleonardi/nanocompore
License: GPL-3.0
Author: Tommaso Leonardi
Author-email: tom@itm6.xyz
Requires-Python: >=3.6.1
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: bedparse (>=0.2.2,<0.3.0)
Requires-Dist: matplotlib (>=3.1,<4.0)
Requires-Dist: numpy (>=1.16,<2.0)
Requires-Dist: pandas (>=0.24.2,<0.25.0)
Requires-Dist: pyfaidx (>=0.5.5,<0.6.0)
Requires-Dist: pyyaml (>=5.1,<6.0)
Requires-Dist: scikit-learn (>=0.21.2,<0.22.0)
Requires-Dist: scipy (>=1.2,<1.3)
Requires-Dist: seaborn (>=0.9.0,<0.10.0)
Requires-Dist: statsmodels (>=0.9.0,<0.10.0)
Requires-Dist: tqdm (>=4.32,<5.0)
Project-URL: Documentation, http://nanocompore.rna.rocks
Project-URL: Repository, https://github.com/tleonardi/nanocompore
Description-Content-Type: text/markdown

![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)
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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

