fastdfe

Fast and flexible inference of the distribution of fitness effects (DFE), VCF-SFS parsing with ancestral allele and site-degeneracy annotation.

https://github.com/sendrowski/fastdfe

Science Score: 57.0%

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 3 DOI reference(s) in README
○
Academic publication links
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (8.3%) to scientific vocabulary

Keywords

ancestral-allele-annotation distribution-of-fitness-effects site-degeneracy-annotation site-frequency-spectrum-parsing

Last synced: 6 months ago · JSON representation ·

Repository

Fast and flexible inference of the distribution of fitness effects (DFE), VCF-SFS parsing with ancestral allele and site-degeneracy annotation.

Basic Info

Host: GitHub
Owner: Sendrowski
License: gpl-3.0
Language: Python
Default Branch: master
Homepage: https://fastdfe.readthedocs.io
Size: 1.14 GB

Statistics

Stars: 17
Watchers: 2
Forks: 0
Open Issues: 1
Releases: 21

Topics

ancestral-allele-annotation distribution-of-fitness-effects site-degeneracy-annotation site-frequency-spectrum-parsing

Created almost 3 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

fastDFE

fastdfe is a package for fast, flexible, and hierarchical inference of the distribution of fitness effects (DFE) from site frequency spectra (SFS). It also contains a versatile VCF-to-SFS parser with support for ancestral allele and site-degeneracy annotation.

Please see the documentation for all the details.

Owner

Name: Janek Sendrowski
Login: Sendrowski
Kind: user
Location: Aarhus
Company: Aarhus University

Repositories: 1
Profile: https://github.com/Sendrowski

Citation (CITATION.md)

```bibtex
@article{fastdfe,
    author = {Sendrowski, Janek and Bataillon, Thomas},
    title = {fastDFE: fast and flexible inference of the distribution of fitness effects},
    journal = {Molecular Biology and Evolution},
    publisher = {Oxford University Press},
    pages = {msae070},
    year = {2024},
    month = {04},
    issn = {1537-1719},
    doi = {10.1093/molbev/msae070},
    url = {https://doi.org/10.1093/molbev/msae070}
}
```

GitHub Events

Total

Create event: 4
Release event: 4
Issues event: 9
Watch event: 6
Issue comment event: 21
Push event: 74

Last Year

Create event: 4
Release event: 4
Issues event: 9
Watch event: 6
Issue comment event: 21
Push event: 74

Dependencies

docs/requirements.txt pypi

cyvcf2 *
jsonpickle *
matplotlib *
mpmath *
multiprocess *
myst-nb *
numpy *
pandas *
pyfaidx *
pyyaml *
scipy *
seaborn *
sphinx *
sphinx-autodoc-typehints *
sphinx-copybutton *
sphinx_rtd_theme *
tqdm *
typing-extensions *

poetry.lock pypi

click 8.1.3
colorama 0.4.6
coloredlogs 15.0.1
contourpy 1.0.7
cycler 0.11.0
cyvcf2 0.30.18
dill 0.3.6
fonttools 4.39.3
humanfriendly 10.0
jsonpickle 3.0.1
kiwisolver 1.4.4
matplotlib 3.7.1
mpmath 1.3.0
multiprocess 0.70.14
numpy 1.24.3
packaging 23.1
pandas 2.0.1
pillow 9.5.0
pyfaidx 0.7.2.1
pyparsing 3.0.9
pyreadline3 3.4.1
python-dateutil 2.8.2
pytz 2023.3
pyyaml 6.0
scipy 1.10.1
seaborn 0.12.2
setuptools 67.7.2
six 1.16.0
tqdm 4.65.0
typing-extensions 4.5.0
tzdata 2023.3

pyproject.toml pypi

cyvcf2 ^0.30.9
jsonpickle ^3.0.0
matplotlib ^3.7.0
mpmath ^1.3.0
multiprocess ^0.70.12
numpy ^1.24.0
pandas ^2.0.0
pyfaidx ^0.7.1
python >=3.10,<3.12
pyyaml ^6.0
scipy ^1.9.3
seaborn ^0.12.0
tqdm ^4.60.0
typing-extensions ^4.5.0

.github/workflows/pip-publish.yml actions

JRubics/poetry-publish v1.16 composite
actions/checkout v3 composite

.github/workflows/pip-test-publish.yml actions

JRubics/poetry-publish v1.16 composite
actions/checkout v3 composite

.github/workflows/run-tests-different-os.yml actions

actions/checkout v3 composite
actions/setup-python v2 composite
codecov/codecov-action v3 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/run-tests.yml actions

actions/checkout v3 composite
codecov/codecov-action v3 composite
conda-incubator/setup-miniconda v2 composite

DESCRIPTION cran

RColorBrewer * imports
cowplot * imports
ggplot2 * imports
grDevices * imports
pheatmap * imports
reticulate * imports
scales * imports
testthat * suggests

snakemake/envs/requirements.txt pypi

biopython ==1.81
certifi ==2024.2.2
charset-normalizer ==3.3.2
click ==8.1.7
colorama ==0.4.6
coloredlogs ==15.0.1
contourpy ==1.2.0
cycler ==0.12.1
cyvcf2 ==0.30.28
dill ==0.3.8
fonttools ==4.49.0
humanfriendly ==10.0
idna ==3.6
jsonpickle ==3.0.3
kiwisolver ==1.4.5
matplotlib ==3.8.3
mpmath ==1.3.0
multiprocess ==0.70.16
numpy ==1.26.4
packaging ==24.0
pandas ==2.2.1
pillow ==10.2.0
pyparsing ==3.1.2
pyreadline3 ==3.4.1
python-dateutil ==2.9.0.post0
pytz ==2024.1
pyyaml ==6.0.1
requests ==2.31.0
scipy ==1.12.0
seaborn ==0.13.2
six ==1.16.0
tqdm ==4.66.2
typing-extensions ==4.10.0
tzdata ==2024.1
urllib3 ==1.26.18

snakemake/envs/requirements_testing.txt pypi

alabaster ==0.7.16 test
appnope ==0.1.4 test
asttokens ==2.4.1 test
attrs ==23.2.0 test
babel ==2.14.0 test
biopython ==1.81 test
certifi ==2024.2.2 test
cffi ==1.16.0 test
charset-normalizer ==3.3.2 test
click ==8.1.7 test
colorama ==0.4.6 test
coloredlogs ==15.0.1 test
comm ==0.2.1 test
contourpy ==1.2.0 test
cycler ==0.12.1 test
cyvcf2 ==0.30.28 test
debugpy ==1.8.1 test
decorator ==5.1.1 test
dill ==0.3.8 test
docutils ==0.17.1 test
exceptiongroup ==1.2.0 test
executing ==2.0.1 test
fastjsonschema ==2.19.1 test
fonttools ==4.49.0 test
greenlet ==3.0.3 test
humanfriendly ==10.0 test
idna ==3.6 test
imagesize ==1.4.1 test
importlib-metadata ==7.0.2 test
ipykernel ==6.29.3 test
ipython ==8.22.2 test
jedi ==0.19.1 test
jinja2 ==3.1.3 test
jsonpickle ==3.0.3 test
jsonschema ==4.21.1 test
jsonschema-specifications ==2023.12.1 test
jupyter-cache ==0.6.1 test
jupyter-client ==8.6.0 test
jupyter-core ==5.7.1 test
kiwisolver ==1.4.5 test
latexcodec ==3.0.0 test
markdown-it-py ==2.2.0 test
markupsafe ==2.1.5 test
matplotlib ==3.8.3 test
matplotlib-inline ==0.1.6 test
mdit-py-plugins ==0.3.5 test
mdurl ==0.1.2 test
mpmath ==1.3.0 test
multiprocess ==0.70.16 test
myst-nb ==0.17.2 test
myst-parser ==0.18.1 test
nbclient ==0.7.4 test
nbformat ==5.9.2 test
nest-asyncio ==1.6.0 test
numpy ==1.26.4 test
packaging ==24.0 test
pandas ==2.2.1 test
parso ==0.8.3 test
pexpect ==4.9.0 test
pillow ==10.2.0 test
platformdirs ==4.2.0 test
prompt-toolkit ==3.0.43 test
psutil ==5.9.8 test
ptyprocess ==0.7.0 test
pure-eval ==0.2.2 test
pybtex ==0.24.0 test
pybtex-docutils ==1.0.3 test
pycparser ==2.21 test
pygments ==2.17.2 test
pyparsing ==3.1.2 test
pyreadline3 ==3.4.1 test
python-dateutil ==2.9.0.post0 test
pytz ==2024.1 test
pywin32 ==306 test
pyyaml ==6.0.1 test
pyzmq ==25.1.2 test
referencing ==0.33.0 test
requests ==2.31.0 test
rpds-py ==0.18.0 test
scipy ==1.12.0 test
seaborn ==0.13.2 test
six ==1.16.0 test
snowballstemmer ==2.2.0 test
sphinx ==5.3.0 test
sphinx-autodoc-typehints ==1.23.0 test
sphinx-copybutton ==0.5.2 test
sphinx-rtd-theme ==1.3.0 test
sphinxcontrib-applehelp ==1.0.8 test
sphinxcontrib-bibtex ==2.6.2 test
sphinxcontrib-devhelp ==1.0.6 test
sphinxcontrib-htmlhelp ==2.0.5 test
sphinxcontrib-jquery ==4.1 test
sphinxcontrib-jsmath ==1.0.1 test
sphinxcontrib-qthelp ==1.0.7 test
sphinxcontrib-serializinghtml ==1.1.10 test
sqlalchemy ==2.0.28 test
stack-data ==0.6.3 test
tabulate ==0.9.0 test
tornado ==6.4 test
tqdm ==4.66.2 test
traitlets ==5.14.1 test
typing-extensions ==4.10.0 test
tzdata ==2024.1 test
urllib3 ==1.26.18 test
wcwidth ==0.2.13 test
zipp ==3.17.0 test

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science