Data structures, algorithms and educational resources for bioinformatics.
Project description
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\__ \ (__| | <| | |_ | |_) | | (_) |
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Opisthokonta
\ Amoebozoa
\ /
* Euryarchaeota
\ |_ Crenarchaeota
\ *
\ /
*
/
/
/
*
/ \
/ \
Proteobacteria \
Cyanobacteria
Core objects, functions and statistics for working with biological data in Python.
To view scikit-bio’s documentation, visit scikit-bio.org.
Note: scikit-bio is currently under active development and its API is not stable. Major compatibility-breaking API changes will likely happen as development progresses. Once the API has started to solidify and we have an official release, we will strive to maintain backwards compatibility, provide deprecation warnings, etc. wherever possible. In the mean time, feel free to try out scikit-bio and let us know what you think!
Licensing
scikit-bio is available under the new BSD license. See COPYING.txt for scikit-bio’s license, and the licenses directory for the licenses of other software that is (either partially or entirely) distributed with scikit-bio.
Installation
In order to install scikit-bio:
pip install numpy pip install scikit-bio
If you’d like to install the dependencies manually (or some other way than using pip), you can find those here:
Projects using scikit-bio
If you’re using scikit-bio in your own projects, you should issue a pull request adding them to this list.
scikit-bio development
If you’re interested in getting involved in or learning about scikit-bio development, see CONTRIBUTING.md, in this directory.
See the list of all of scikit-bio’s contributors.
Summaries of our weekly developer meetings are posted on HackPad. Click here to view the meeting notes for 2014.
The pre-history of scikit-bio
scikit-bio began from code derived from PyCogent and QIIME, and the contributors and/or copyright holders have agreed to make the code they wrote for PyCogent and/or QIIME available under the BSD license. The contributors to PyCogent and/or QIIME modules that have been ported to scikit-bio are: Rob Knight (@rob-knight), Gavin Huttley (@gavin-huttley), Daniel McDonald (@wasade), Micah Hamady, Antonio Gonzalez (@antgonza), Sandra Smit, Greg Caporaso (@gregcaporaso), Jai Ram Rideout (@ElBrogrammer), Cathy Lozupone (@clozupone), Mike Robeson (@mikerobeson), Marcin Cieslik, Peter Maxwell, Jeremy Widmann, Zongzhi Liu, Michael Dwan, Logan Knecht (@loganknecht), Andrew Cochran, Jose Carlos Clemente (@cleme), Damien Coy, Levi McCracken, Andrew Butterfield, Will Van Treuren (@wdwvt1), Justin Kuczynski (@justin212k), and Jose Antonio Navas Molina (@josenavas).
Logo
scikit-bio ASCII art created by @gregcaporaso. Text logo created at patorjk.com.
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