Polarize genomes using diem
Project description
diemPy
A Python package for genome polarization and subsequent analyses using the diem (Diagnostic Index for the Expectation Maximization) method [1]
Overview
diemPy is a computational tool designed to polarize genomic data for hybrid zone analysis. The package implements an expectation-maximization (EM) algorithm to determine the optimal polarization of genetic markers, enabling researchers to identify and analyze patterns of introgression and hybridization in genomic datasets.
Key Features
- VCF processing and format conversion
- Automated genome polarization using EM algorithm
- Kernel smoothing and tract length analysis
- Parallel processing support
- Flexible I/O for various genomic formats
Documentation
The core concepts, installation, and API documentation can be found here:
📚 Introduction, Installation, and API Documentation
The primary documentation for using diemPy is provided as a self-guided tutorial with an example dataset:
📚 Tutorial
License
This project is licensed under the GPL-3.0 License - see the LICENSE file for details.
Author
Derek Setter, Stuart J.E. Baird
Citation
[1] Baird, S. J. E., Petružela, J., Jaroň, I., Škrabánek, P., & Martínková, N. (2023). Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution, 14, 512–528. https://doi.org/10.1111/2041-210X.14010
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file diempy-1.0.2.tar.gz.
File metadata
- Download URL: diempy-1.0.2.tar.gz
- Upload date:
- Size: 101.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
3fe3f8b24552b3cdb5f50fb2a3e85c1b50a7ed617f340be01293a45bb99b235c
|
|
| MD5 |
60c217ab8603d60ac4dd9f1ecdbc50ad
|
|
| BLAKE2b-256 |
4b29c0a9e25ee4c70fbc0da603e60ed23d54482e3dfad7a55964e8ac46e8de3e
|
Provenance
The following attestation bundles were made for diempy-1.0.2.tar.gz:
Publisher:
python-publish.yml on Studenecivb/diemPy
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
diempy-1.0.2.tar.gz -
Subject digest:
3fe3f8b24552b3cdb5f50fb2a3e85c1b50a7ed617f340be01293a45bb99b235c - Sigstore transparency entry: 1171903043
- Sigstore integration time:
-
Permalink:
Studenecivb/diemPy@75746083bfd91813654506e312fcf098091f9a0f -
Branch / Tag:
refs/tags/v1.0.2 - Owner: https://github.com/Studenecivb
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
python-publish.yml@75746083bfd91813654506e312fcf098091f9a0f -
Trigger Event:
release
-
Statement type:
File details
Details for the file diempy-1.0.2-py3-none-any.whl.
File metadata
- Download URL: diempy-1.0.2-py3-none-any.whl
- Upload date:
- Size: 105.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
a2c4e066317c1c9c15c4f6dae36ac6c26cd9e37be025738106a766e8f9025e9c
|
|
| MD5 |
a063df174c8d5167a7bdac88929ab211
|
|
| BLAKE2b-256 |
856cf9710f45127dd6f0e20386b6504ff5969ea77e89315960e491caa986017e
|
Provenance
The following attestation bundles were made for diempy-1.0.2-py3-none-any.whl:
Publisher:
python-publish.yml on Studenecivb/diemPy
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
diempy-1.0.2-py3-none-any.whl -
Subject digest:
a2c4e066317c1c9c15c4f6dae36ac6c26cd9e37be025738106a766e8f9025e9c - Sigstore transparency entry: 1171903046
- Sigstore integration time:
-
Permalink:
Studenecivb/diemPy@75746083bfd91813654506e312fcf098091f9a0f -
Branch / Tag:
refs/tags/v1.0.2 - Owner: https://github.com/Studenecivb
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
python-publish.yml@75746083bfd91813654506e312fcf098091f9a0f -
Trigger Event:
release
-
Statement type:
