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nanocount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

https://github.com/a-slide/nanocount

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

Basic Info
Statistics
  • Stars: 63
  • Watchers: 2
  • Forks: 6
  • Open Issues: 1
  • Releases: 25
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct

README.md

NanoCount v1.1.0.post2

NanoCount

GitHub license Language DOI Build Status

PyPI version PyPI downloads Anaconda Version

Anaconda Downloads

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/

Disclaimer

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.

Thank you

citation

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

licence

MIT (https://mit-license.org/)

Copyright © 2020 Adrien Leger

Authors

  • Adrien Leger / aleg@ebi.ac.uk / https://adrienleger.com

The package was inspired from https://github.com/jts/nanopore-rna-analysis by Jared Simpson

  • Jared Simpson (@jts)

Classifiers

  • Development Status :: 3 - Alpha
  • Intended Audience :: Science/Research
  • Topic :: Scientific/Engineering :: Bio-Informatics
  • License :: OSI Approved :: MIT License
  • Programming Language :: Python :: 3

Owner

  • Name: Adrien Leger
  • Login: a-slide
  • Kind: user
  • Location: Oxford, UK
  • Company: @nanoporetech

Research scientist at Oxford Nanopore Technologies

GitHub Events

Total
  • Issues event: 3
  • Watch event: 9
  • Issue comment event: 2
Last Year
  • Issues event: 3
  • Watch event: 9
  • Issue comment event: 2

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 103
  • Total Committers: 4
  • Avg Commits per committer: 25.75
  • Development Distribution Score (DDS): 0.184
Past Year
  • Commits: 5
  • Committers: 3
  • Avg Commits per committer: 1.667
  • Development Distribution Score (DDS): 0.4
Top Committers
Name Email Commits
a-slide a****r@n****m 84
Josie Gleeson 3****n 17
Tommaso Leonardi t****m@i****z 1
TheChymist 1****t 1
Committer Domains (Top 20 + Academic)
itm6.xyz: 1 nanoporetech.com: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 38
  • Total pull requests: 6
  • Average time to close issues: 4 months
  • Average time to close pull requests: less than a minute
  • Total issue authors: 26
  • Total pull request authors: 2
  • Average comments per issue: 1.71
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 1
  • Average time to close issues: 25 days
  • Average time to close pull requests: less than a minute
  • Issue authors: 6
  • Pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rezarahman12 (4)
  • vetmohit89 (3)
  • callumparr (3)
  • kerenzhou062 (2)
  • a-slide (2)
  • josiegleeson (2)
  • lpryszcz (1)
  • reJELIN (1)
  • M-Chi-1 (1)
  • ms-gx (1)
  • zhenyu7500 (1)
  • NStrowbridge (1)
  • camillaugolini-iit (1)
  • corneliusroemer (1)
  • chloebonenfant (1)
Pull Request Authors
  • josiegleeson (4)
  • a-slide (3)
Top Labels
Issue Labels
bug (3) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 51 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 25
  • Total maintainers: 1
pypi.org: nanocount

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

  • Versions: 25
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 51 Last month
Rankings
Stargazers count: 10.0%
Dependent packages count: 10.0%
Forks count: 15.3%
Average: 15.9%
Dependent repos count: 21.7%
Downloads: 22.7%
Maintainers (1)
aleg
Last synced: 7 months ago

Dependencies

.versipy/setup.py pypi
  • dependency_1__ *
setup.py pypi
  • tqdm >=4.51.0
.github/workflows/python-publish.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v3 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite