NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA sequencing* datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads
NanoCount estimates transcripts abundance from Oxford Nanopore direct-RNA sequencing datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads
Full documentation is available at https://a-slide.github.io/NanoCount/
Please be aware that NanoCount is a research package that is still under development.
The API, command line interface, and implementation might change without retro-compatibility.
It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.
The repository is archived at Zenodo. If you use NanoCount please cite as follow:
Josie Gleeson, Adrien Leger, Yair D J Prawer, Tracy A Lane, Paul J Harrison, Wilfried Haerty, Michael B Clark, Accurate expression quantification from nanopore direct RNA sequencing with NanoCount, Nucleic Acids Research, 2021;, gkab1129, https://doi.org/10.1093/nar/gkab1129
Copyright © 2020 Adrien Leger
The package was inspired from https://github.com/jts/nanopore-rna-analysis by Jared Simpson
- Jared Simpson (@jts)
- Development Status :: 3 - Alpha
- Intended Audience :: Science/Research
- Topic :: Scientific/Engineering :: Bio-Informatics
- License :: OSI Approved :: MIT License
- Programming Language :: Python :: 3
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