mutyper

mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra - Published in JOSS (2023)

https://github.com/harrispopgen/mutyper

Science Score: 100.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
1 of 6 committers (16.7%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Scientific Fields

Biology Life Sciences - 63% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Ancestral k-mer mutation types for SNP data

Basic Info

Host: GitHub
Owner: harrispopgen
License: mit
Language: Python
Default Branch: master
Homepage: https://harrispopgen.github.io/mutyper/
Size: 6.21 MB

Statistics

Stars: 8
Watchers: 2
Forks: 4
Open Issues: 6
Releases: 24

Created almost 6 years ago · Last pushed over 2 years ago

Metadata Files

Readme Contributing License Citation

README.md

A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs

See documentation for install and usage information.

Pairs well with the package mushi, which performs mutation spectrum history inference.

Owner

Name: harrispopgen
Login: harrispopgen
Kind: organization

Repositories: 3
Profile: https://github.com/harrispopgen

JOSS Publication

mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra

Published

May 10, 2023

DOI

10.21105/joss.05227

Volume 8, Issue 85, Page 5227

Authors

William S. DeWitt

Department of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, United States of America

Luke Zhu

Department of Bioengineering, University of Washington, Seattle, WA, United States of America

Mitchell R. Vollger

Department of Genome Sciences, University of Washington, Seattle, WA, United States of America

Michael E. Goldberg

Department of Genome Sciences, University of Washington, Seattle, WA, United States of America, Departments of Human Genetics and of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States of America

Andrea Talenti

The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom

Annabel C. Beichman

Department of Genome Sciences, University of Washington, Seattle, WA, United States of America

Kelley Harris

Department of Genome Sciences, University of Washington, Seattle, WA, United States of America

Editor

Lorena Pantano

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: DeWitt
  given-names: William S.
  orcid: "https://orcid.org/0000-0002-6802-9139"
- family-names: Zhu
  given-names: Luke
  orcid: "https://orcid.org/0000-0002-6324-1464"
- family-names: Vollger
  given-names: Mitchell R.
  orcid: "https://orcid.org/0000-0002-8651-1615"
- family-names: Goldberg
  given-names: Michael E.
  orcid: "https://orcid.org/0000-0003-3310-6349"
- family-names: Talenti
  given-names: Andrea
  orcid: "https://orcid.org/0000-0003-1309-3667"
- family-names: Beichman
  given-names: Annabel C.
  orcid: "https://orcid.org/0000-0002-6991-587X"
- family-names: Harris
  given-names: Kelley
  orcid: "https://orcid.org/0000-0003-0302-2523"
contact:
- family-names: DeWitt
  given-names: William S.
  orcid: "https://orcid.org/0000-0002-6802-9139"
doi: 10.5281/zenodo.7921769
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: DeWitt
    given-names: William S.
    orcid: "https://orcid.org/0000-0002-6802-9139"
  - family-names: Zhu
    given-names: Luke
    orcid: "https://orcid.org/0000-0002-6324-1464"
  - family-names: Vollger
    given-names: Mitchell R.
    orcid: "https://orcid.org/0000-0002-8651-1615"
  - family-names: Goldberg
    given-names: Michael E.
    orcid: "https://orcid.org/0000-0003-3310-6349"
  - family-names: Talenti
    given-names: Andrea
    orcid: "https://orcid.org/0000-0003-1309-3667"
  - family-names: Beichman
    given-names: Annabel C.
    orcid: "https://orcid.org/0000-0002-6991-587X"
  - family-names: Harris
    given-names: Kelley
    orcid: "https://orcid.org/0000-0003-0302-2523"
  date-published: 2023-05-10
  doi: 10.21105/joss.05227
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5227
  title: "mutyper: assigning and summarizing mutation types for
    analyzing germline mutation spectra"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05227"
  volume: 8
title: "`mutyper`: assigning and summarizing mutation types for
  analyzing germline mutation spectra"

GitHub Events

Total

Watch event: 1
Issue comment event: 1
Fork event: 1

Last Year

Watch event: 1
Issue comment event: 1
Fork event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 128
Total Committers: 6
Avg Commits per committer: 21.333
Development Distribution Score (DDS): 0.063

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
William DeWitt	w**t@g**m	120
Lukez-pi	l**4@g**m	3
Mitchell Robert Vollger	m**r@g**m	2
goldmich	3****h	1
RenzoTale88	2****8	1
Andrea Talenti	a**i@e**k	1

Committer Domains (Top 20 + Academic)

ed.ac.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 25
Total pull requests: 25
Average time to close issues: about 2 months
Average time to close pull requests: 1 day
Total issue authors: 9
Total pull request authors: 5
Average comments per issue: 1.96
Average comments per pull request: 0.44
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

WSDeWitt (9)
izabelcavassim (5)
RenzoTale88 (2)
ab08028 (2)
Lukez-pi (2)
mrvollger (2)
vladsavelyev (1)
barlavi1 (1)
goldmich (1)

Pull Request Authors

WSDeWitt (17)
Lukez-pi (3)
RenzoTale88 (2)
mrvollger (2)
goldmich (1)

Top Labels

Issue Labels

enhancement (1) bug (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 93 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 23
Total maintainers: 1

pypi.org: mutyper

ancestral k-mer mutation types for SNP data

Homepage: https://github.com/harrispopgen/mutyper
Documentation: https://mutyper.readthedocs.io/
License: MIT License
Latest release: 1.0.2
published over 2 years ago

Versions: 23
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 93 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 16.9%

Stargazers count: 20.4%

Dependent repos count: 21.6%

Average: 22.5%

Downloads: 43.4%

Maintainers (1)

wsdewitt

Last synced: 4 months ago

Dependencies

environment.yml conda

bcftools
pip
tabix

requirements.txt pypi

black *
docformatter *
flake8 *
jupyter *
nbsphinx *
pandas *
pytest *
sphinx *
sphinx-argparse *
sphinx-autodoc-typehints *
sphinx_rtd_theme *
sphinxcontrib-programoutput *

setup.py pypi

biopython *
cyvcf2 >=0.30.15
pandas *
pyfaidx *
pyliftover *

.github/workflows/build-and-test.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite
r-lib/actions/setup-pandoc v2 composite

.github/workflows/docs-build-and-deploy.yml actions

JamesIves/github-pages-deploy-action v4.2.2 composite
actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite
r-lib/actions/setup-pandoc v2 composite

.github/workflows/python-publish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

mutyper

Science Score: 100.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

See documentation for install and usage information.

Owner

JOSS Publication

mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: mutyper

Rankings

Maintainers (1)

Dependencies