haptools

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

https://github.com/cast-genomics/haptools

Science Score: 65.0%

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 2 DOI reference(s) in README
○
Academic publication links
○
Committers with academic emails
✓
Institutional organization owner
Organization cast-genomics has institutional domain (admixgenomics.ucsd.edu)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (7.9%) to scientific vocabulary

Keywords

gwas simulation

Last synced: 6 months ago · JSON representation ·

Repository

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

Basic Info

Host: GitHub
Owner: CAST-genomics
License: mit
Language: Python
Default Branch: main
Homepage: https://haptools.readthedocs.io
Size: 8.75 MB

Statistics

Stars: 24
Watchers: 4
Forks: 4
Open Issues: 16
Releases: 14

Topics

gwas simulation

Created over 4 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License Citation

haptools

Haptools is a collection of tools for simulating and analyzing genotypes and phenotypes while taking into account haplotype information. Haptools supports fast simulation of admixed genomes (with simgenotype), visualization of admixture tracks (with karyogram), simulating haplotype- and local ancestry-specific phenotype effects (with transform and simphenotype), and computing a variety of common file operations and statistics in a haplotype-aware manner.

Homepage: https://haptools.readthedocs.io/

Visit our homepage for installation and usage instructions.

haptools commands

citation

There is an option to "Cite this repository" on the right sidebar of the repository homepage

Arya R Massarat, Michael Lamkin, Ciara Reeve, Amy L Williams, Matteo D’Antonio, Melissa Gymrek, Haptools: a toolkit for admixture and haplotype analysis, Bioinformatics, 2023;, btad104, https://doi.org/10.1093/bioinformatics/btad104

Owner

Name: Center for Admixture Science and Technology
Login: CAST-genomics
Kind: organization

Website: http://admixgenomics.ucsd.edu/
Repositories: 4
Profile: https://github.com/CAST-genomics

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: 'Haptools: a toolkit for admixture and haplotype analysis'
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Arya R
    family-names: Massarat
    affiliation: >-
      Bioinformatics and Systems Biology Graduate Program, Department of Bioengineering, University of California San Diego, La Jolla, 92093, USA
    orcid: 'https://orcid.org/0000-0002-3679-0345'
  - given-names: Michael
    family-names: Lamkin
    affiliation: >-
      Department of Computer Science and Engineering, University of California San Diego, La Jolla, 92093, USA
    orcid: 'https://orcid.org/0000-0000-1579-7191'
  - given-names: Ciara
    family-names: Reeve
    affiliation: >-
      Department of Bioengineering, University of California San Diego, La Jolla, 92093, USA
  - given-names: Amy L
    family-names: Williams
    affiliation: '23andMe, Inc., Sunnyvale, California, 94086, USA'
    orcid: 'https://orcid.org/0000-0003-0737-0533'
  - given-names: Matteo
    family-names: D’Antonio
    affiliation: >-
      Department of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, 92093, USA
    orcid: 'https://orcid.org/0000-0001-5844-6433'
  - given-names: Melissa
    family-names: Gymrek
    email: mgymrek@eng.ucsd.edu
    affiliation: >-
      Department of Computer Science and Engineering, University of California San Diego, La Jolla, 92093, USA & Department of Medicine, University of California San Diego, La Jolla, 92093, USA
    orcid: 'https://orcid.org/0000-0002-6086-3903'
identifiers:
  - type: doi
    value: 10.1093/bioinformatics/btad104
repository-code: 'https://github.com/CAST-genomics/haptools'
url: 'https://haptools.readthedocs.io/'
license: MIT

GitHub Events

Total

Create event: 11
Issues event: 6
Release event: 1
Watch event: 4
Delete event: 11
Issue comment event: 27
Push event: 100
Pull request review event: 13
Pull request review comment event: 2
Pull request event: 21

Last Year

Create event: 11
Issues event: 6
Release event: 1
Watch event: 4
Delete event: 11
Issue comment event: 27
Push event: 100
Pull request review event: 13
Pull request review comment event: 2
Pull request event: 21

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 647
Total Committers: 8
Avg Commits per committer: 80.875
Development Distribution Score (DDS): 0.263

Top Committers

Name	Email	Commits
Arya Massarat	2**m@u**m	477
mlamkin7	m**l@a**m	98
Melissa Gymrek	m**k@M**l	32
Ciara Reeve	7**e@u**m	26
github-actions[bot]	4**]@u**m	5
Matteo	s**9@g**m	4
Melissa Gymrek	m**k@M**t	3
Gymrek Lab	m**k@g**m	2

Committer Domains (Top 20 + Academic)

melissas-mbp.attlocal.net: 1 alamkin.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 30
Total pull requests: 116
Average time to close issues: 2 months
Average time to close pull requests: 9 days
Total issue authors: 8
Total pull request authors: 8
Average comments per issue: 2.3
Average comments per pull request: 0.47
Merged pull requests: 106
Bot issues: 0
Bot pull requests: 12

Past Year

Issues: 2
Pull requests: 4
Average time to close issues: 24 days
Average time to close pull requests: 6 days
Issue authors: 2
Pull request authors: 1
Average comments per issue: 8.0
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

aryarm (22)
gymreklab (2)
drdna (1)
s041629 (1)
KangchengHou (1)
armartin (1)
RJDan (1)
cindywen96 (1)

Pull Request Authors

aryarm (92)
mlamkin7 (27)
github-actions[bot] (17)
gymreklab (2)
amythewilliams (1)
Ayimany (1)
ciarareeve (1)
gonzalogc1 (1)

Top Labels

Issue Labels

enhancement (11) idea (4) documentation (2) large-files (1) bug (1) refactor (1) help wanted (1)

Pull Request Labels

autorelease: tagged (9) autorelease: pending (8) refactor (1)

Packages

Total packages: 1
Total downloads:
- pypi 76 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 11
Total maintainers: 2

pypi.org: haptools

Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis

Homepage: https://github.com/cast-genomics/haptools
Documentation: https://haptools.readthedocs.io
License: MIT
Latest release: 0.5.0
published about 1 year ago

Versions: 11
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 76 Last month

Rankings

Dependent packages count: 10.1%

Stargazers count: 16.0%

Forks count: 19.1%

Average: 19.3%

Dependent repos count: 21.6%

Downloads: 29.7%

Maintainers (2)

mgymrek aryarm

Last synced: 7 months ago

Dependencies

.github/workflows/conventional-prs.yml actions

amannn/action-semantic-pull-request v5.0.2 composite

.github/workflows/release.yml actions

GoogleCloudPlatform/release-please-action v3 composite
actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish v1.5.0 composite

.github/workflows/tests.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite
actions/upload-artifact v3 composite
actionsdesk/lfs-warning v3.2 composite

poetry.lock pypi

appnope 0.1.3 develop
argcomplete 2.0.0 develop
attrs 22.1.0 develop
backcall 0.2.0 develop
black 22.10.0 develop
colorlog 6.7.0 develop
coverage 7.2.7 develop
decorator 5.1.1 develop
distlib 0.3.6 develop
exceptiongroup 1.0.1 develop
filelock 3.8.0 develop
iniconfig 1.1.1 develop
ipython 7.34.0 develop
jedi 0.18.1 develop
matplotlib-inline 0.1.6 develop
mypy-extensions 0.4.3 develop
nox 2022.8.7 develop
nox-poetry 1.0.1 develop
parso 0.8.3 develop
pathspec 0.10.1 develop
pexpect 4.8.0 develop
pickleshare 0.7.5 develop
platformdirs 2.5.3 develop
pluggy 1.0.0 develop
prompt-toolkit 3.0.32 develop
ptyprocess 0.7.0 develop
py 1.11.0 develop
pytest 7.2.0 develop
tomlkit 0.11.6 develop
traitlets 5.5.0 develop
typed-ast 1.5.4 develop
virtualenv 20.16.6 develop
wcwidth 0.2.5 develop
alabaster 0.7.12
babel 2.11.0
certifi 2022.9.24
charset-normalizer 2.1.1
click 8.1.3
colorama 0.4.6
coloredlogs 15.0.1
cycler 0.11.0
cython 3.0.0
cyvcf2 0.30.18
docutils 0.17.1
fonttools 4.38.0
humanfriendly 10.0
idna 3.4
imagesize 1.4.1
importlib-metadata 4.13.0
jinja2 3.1.2
kiwisolver 1.4.4
markupsafe 2.1.1
matplotlib 3.5.3
numpy 1.21.6
numpydoc 1.5.0
packaging 21.3
pgenlib 0.90.1
pillow 9.3.0
pygments 2.13.0
pyparsing 3.0.9
pyreadline 2.1
pyreadline3 3.4.1
pysam 0.21.0
python-dateutil 2.8.2
pytz 2022.6
requests 2.28.1
setuptools-scm 6.4.2
six 1.16.0
snowballstemmer 2.2.0
sphinx 5.3.0
sphinx-autodoc-typehints 1.19.5
sphinx-click 4.3.0
sphinx-rtd-theme 1.1.1
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
tomli 2.0.1
typing-extensions 4.4.0
urllib3 1.26.12
zipp 3.10.0

pyproject.toml pypi

Sphinx >=4.3.2 develop
black >=22.3.0 develop
coverage >=6.5.0 develop
ipython >=7.30.1 develop
nox >=2022.8.7 develop
nox-poetry >=1.0.1 develop
numpydoc >=1.1.0 develop
pytest >=6.2.5 develop
sphinx-autodoc-typehints >=1.12.0 develop
sphinx-click >=3.0.2 develop
sphinx-rtd-theme >=1.0.0 develop
Pgenlib >=0.90.1
Sphinx >=4.3.2
click >=8.0.3
cyvcf2 >=0.30.14
matplotlib >=3.5.1
numpy >=1.20.0
numpydoc >=1.1.0
pysam >=0.19.0
python >=3.7,<3.11
sphinx-autodoc-typehints >=1.12.0
sphinx-click >=3.0.2
sphinx-rtd-theme >=1.0.0

haptools

Science Score: 65.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

haptools

citation

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

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: haptools

Rankings

Maintainers (2)

Dependencies