https://github.com/bio2bel/msig
Integration of pathway-related information from MSigDB in BEL
https://github.com/bio2bel/msig
gene-set-enrichment msig msigdb pathway-analysis
Last synced: 4 months ago
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Integration of pathway-related information from MSigDB in BEL
- Host: GitHub
- URL: https://github.com/bio2bel/msig
- Owner: bio2bel
- License: mit
- Created: 2018-03-05T16:40:55.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2020-11-18T12:50:12.000Z (over 5 years ago)
- Last Synced: 2026-01-03T13:43:01.846Z (5 months ago)
- Topics: gene-set-enrichment, msig, msigdb, pathway-analysis
- Language: Python
- Homepage: http://bio2bel-msig.rtfd.io/
- Size: 66.4 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
Bio2BEL MSigDB |build| |coverage| |documentation| |zenodo|
==========================================================
This package allows the enrichment of BEL networks with MSigDB information.
Furthermore, it is integrated in the `ComPath environment `_ for pathway database comparison.
If you find this package useful, please consider citing [domingofernandez2018]_:
.. [domingofernandez2018] Domingo-Fernandez, D., *et al* (2018). `ComPath: an ecosystem for exploring, analyzing,
and curating mappings across pathway databases `_.
*Npj Systems Biology and Applications*, __5__(1), 3.
**Warning** This package creates ``partOf`` relationships in BEL. MSigDB does not contain mechanistic relationships,
but it include simplifications of several sources (KEGG, WikiPathways, Reactome, PID) that do have mechanistic
relationships. Those sources can be converted to BEL with the
`PathMe project `_.
Installation |pypi_version| |python_versions| |pypi_license|
------------------------------------------------------------
``bio2bel_msig`` can be installed easily from `PyPI `_ with the
following code in your favorite terminal:
.. code-block:: sh
$ pip install bio2bel_msig
or from the latest code on `GitHub `_ in development mode with:
.. code-block:: sh
$ git clone https://github.com/bio2bel/msig.git
$ cd msig
$ pip install -e .
Setup
-----
The package expects you have downloaded the gene sets from MSigDB following the instructions and terms stated in
their `website `_.
The environment variable `BIO2BEL_MSIG_PATH` should be set to the directory where the gene set files in the GMT format
are stored. Optionally, this can be directly overridden with the keyword argument to `populate()` in the REPL or as
a flag in the command line utility.
Python REPL
~~~~~~~~~~~
.. code-block:: python
>>> import bio2bel_msig
>>> msig_manager = bio2bel_msig.Manager()
>>> msig_manager.populate()
Command Line Utility
~~~~~~~~~~~~~~~~~~~~
.. code-block:: bash
bio2bel_msig populate
Other Command Line Utilities
----------------------------
- Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_msig web` (http://localhost:5000/admin/)
- Export gene sets for programmatic use :code:`python3 -m bio2bel_msig export`
Citation
--------
- Subramanian, A., *et al.* (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550.
- Liberzon, A., *et al* (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739-1740.
.. |build| image:: https://travis-ci.org/bio2bel/msig.svg?branch=master
:target: https://travis-ci.org/bio2bel/msig
:alt: Build Status
.. |coverage| image:: https://codecov.io/gh/bio2bel/msig/coverage.svg?branch=master
:target: https://codecov.io/gh/bio2bel/msig?branch=master
:alt: Coverage Status
.. |documentation| image:: http://readthedocs.org/projects/bio2bel-msig/badge/?version=latest
:target: http://bio2bel.readthedocs.io/projects/msig/en/latest/?badge=latest
:alt: Documentation Status
.. |climate| image:: https://codeclimate.com/github/bio2bel/msig/badges/gpa.svg
:target: https://codeclimate.com/github/bio2bel/msig
:alt: Code Climate
.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_msig.svg
:alt: Stable Supported Python Versions
.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_msig.svg
:alt: Current version on PyPI
.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_msig.svg
:alt: MIT License
.. |zenodo| image:: https://zenodo.org/badge/123948554.svg
:target: https://zenodo.org/badge/latestdoi/123948554