https://github.com/dcdanko/gimmebio
https://github.com/dcdanko/gimmebio
Last synced: 4 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/dcdanko/gimmebio
- Owner: dcdanko
- License: mit
- Created: 2017-08-16T17:34:00.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2022-12-26T20:44:28.000Z (over 3 years ago)
- Last Synced: 2025-04-12T14:51:56.062Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 44.7 MB
- Stars: 2
- Watchers: 1
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
gimmebio
========
.. image:: https://img.shields.io/pypi/v/gimmebio.svg
:target: https://pypi.python.org/pypi/gimmebio
.. image:: https://circleci.com/gh/dcdanko/gimmebio.svg?style=svg
:target: https://circleci.com/gh/dcdanko/gimmebio
.. image:: https://www.codefactor.io/Content/badges/A.svg
:target: https://www.codefactor.io/repository/github/dcdanko/gimmebio
Utilities and explorations in computational Biology. MIT License.
Packages
--------
- Kmers, make kmers of many different styles.
- Linked Reads, utilities for handling linked read data
- Seqs, general utilites for handling sequence data. Some IO which should be deprecated
- Bayesian First Aid, incomplete python implementation of bfa_
- Hiveplots, python implemnetation of hiveplots with area hiveplots
- operonator, experiment using linked reads to detect gene clusters
- ponce_de_leon, experiment using Approx Bayesian Computation to bridge low complexity regiosn
- ram_seq, use Ramanujan-Fourier transform to process sequence data
- seqtalk, experiment with neural nets for sequence processing
- taxa_ags_normalizer, estimate average genome size for taxa
Installation
------------
Install from PyPi.
.. code-block:: bash
pip install gimmebio
Install from source.
.. code-block:: bash
git clone git@github.com:dcdanko/gimmebio.git
cd gimmebio
python setup.py install
Credits
-------
This package is structured as a set of microlibraries_
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
`gimmebio` was written by `David C. Danko `_.
.. _bfa: https://github.com/rasmusab/bayesian_first_aid
.. _metadata: https://github.com/MetaSUB/MetaSUB-metadata
.. _metagenscope: https://www.metagenscope.com/
.. _microlibraries: https://blog.shazam.com/python-microlibs-5be9461ad979
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _AWS-CLI: https://docs.aws.amazon.com/cli/latest/userguide/installing.html