This release has been yanked by its maintainers, and will be ignored by installers, except when explicitly specified.
Consider using release 0.0.16a19 instead.
Reason given by maintainers: reason: Ships no trained classifiers; superseded by 0.0.5a2.
Copyright (c) 2019-2025 - President and Fellows of Harvard College. All rights reserved.
SigMA2 - Mutational Signature Analysis in Python
SigMA2 is the Python version of SigMA, a tool developed to detect mutational Signature 3, which is associated with homologous recombination (HR) deficiency. It supports hybrid capture panels, whole-exome, and whole-genome sequencing (WGS) data. While traditional signature analysis tools struggle with data containing few single nucleotide variants (SNVs), SigMA2 is designed to perform well in such settings.
Installation
From PyPI (Recommended)
#pip install sigma2 # currently unavailable
From Source
git clone https://github.com/sigscape/SigMA2.git
conda env create -f ./SigMA2/environment.yml
conda activate sigmapy310
pip install -e ./SigMA2
Quick Start
Follow these Jupyter Notebooks in numerical order to get started with SigMA2 and its built-in functions!
Documentation & Further Information
Find more here
Contact
Requests for use of the Software for or on behalf of for-profit entities or for any commercial purposes, please contact:
Office of Technology Development Harvard University Smith Campus Center, Suite 727E 1350 Massachusetts Avenue Cambridge, MA 02138 USA Telephone: (617) 495-3067 E-mail: otd@harvard.edu
Citation
If you use SigMA2 in your work, please cite the original SigMA publication as follows:
Detecting the mutational signature of homologous recombination deficiency in clinical samples
<br/>Doga C. Gulhan, Jake June-Koo Lee, Giorgio E. M. Melloni, Isidro Cortés-Ciriano & Peter J. Park<br/>Nature Genetics (2019)<br/>https://doi.org/10.1038/s41588-019-0390-2
1 maintainer
Metadata
1 maintainer
Release files for sigma2 0.0.4a0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| sigma2-0.0.4a0.tar.gz | 13.7 MB | With provenance | Details for sigma2-0.0.4a0.tar.gz |
Built distributions (wheels)
| File | Actions Reset | |||
|---|---|---|---|---|
| sigma2-0.0.4a0-cp39-abi3-win_amd64.whl | CPython 3.9 | abi3 | Windows x86-64 | Details for sigma2-0.0.4a0-cp39-abi3-win_amd64.whl |
| sigma2-0.0.4a0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.9 | abi3 | Linux glibc 2.17+ x86-64 | Details for sigma2-0.0.4a0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
| sigma2-0.0.4a0-cp39-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.9 | abi3 | Linux glibc 2.17+ ARM64 | Details for sigma2-0.0.4a0-cp39-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
| sigma2-0.0.4a0-cp39-abi3-macosx_11_0_arm64.whl | CPython 3.9 | abi3 | macOS 11.0+ ARM64 | Details for sigma2-0.0.4a0-cp39-abi3-macosx_11_0_arm64.whl |
Total release size: 69.2 MB
Release files / sigma2-0.0.4a0.tar.gz
| Download URL | sigma2-0.0.4a0.tar.gz |
|---|---|
| Size | 13.7 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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| Download URL | sigma2-0.0.4a0-cp39-abi3-win_amd64.whl |
|---|---|
| Size | 13.8 MB |
| Tags | CPython 3.9 Windows x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
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| Download URL | sigma2-0.0.4a0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 13.9 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
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| Uploaded via |
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| Download URL | sigma2-0.0.4a0-cp39-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 13.9 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ ARM64 abi3 |
|
SHA-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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| Download URL | sigma2-0.0.4a0-cp39-abi3-macosx_11_0_arm64.whl |
|---|---|
| Size | 13.9 MB |
| Tags | CPython 3.9 abi3 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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