Note: scikit-bio is no longer compatible with Python 2. scikit-bio is compatible with Python 3.6 and later.
scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.
Installing
The recommended way to install scikit-bio is via the
conda package manager available in Anaconda or miniconda.
Download: Download full-size image Fig. The one-way ANOVA results for torque acting on the tractor from the plough (MxIMPL) and rear wheel load difference (RWLD = FzCTRR – FzCTRL), right-hand ploughing; vertical columns represent confidence intervals at a 95% significance level.
To install the latest release of scikit-bio:
Alternatively, you can install scikit-bio using
pip :
You can verify your installation by running the scikit-bio unit tests:
For users of Debian,
skbio is in the Debian software distribution and maybe installed using:
Getting help
To get help with scikit-bio, you should use the skbio tag on StackOverflow (SO). Before posting a question, check out SO's guide on how to ask a question. The scikit-bio developers regularly monitor the
skbio SO tag.
Projects using scikit-bio
Some of the projects that we know of that are using scikit-bio are:
If you're using scikit-bio in your own projects, feel free to issue a pull request to add them to this list.
scikit-bio development
If you're interested in getting involved in scikit-bio development, see CONTRIBUTING.md.
See the list of scikit-bio's contributors.
Licensing
scikit-bio is available under the new BSD license. SeeCOPYING.txt for scikit-bio's license, and thelicenses directory for the licenses of third-party software that is(either partially or entirely) distributed with scikit-bio.
The pre-history of scikit-bio
scikit-bio began from code derived from PyCogent and QIIME, andthe contributors and/or copyright holders have agreed to make the codethey wrote for PyCogent and/or QIIME available under the BSDlicense. The contributors to PyCogent and/or QIIME modules that havebeen ported to scikit-bio are: Rob Knight (@rob-knight), Gavin Huttley (@gavin-huttley), Daniel McDonald (@wasade), Micah Hamady, Antonio Gonzalez(@antgonza), Sandra Smit, GregCaporaso (@gregcaporaso), JaiRam Rideout (@jairideout),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), DamienCoy, Levi McCracken, Andrew Butterfield, Will Van Treuren (@wdwvt1), Justin Kuczynski (@justin212k), Jose Antonio Navas Molina(@josenavas), Matthew Wakefield(@genomematt) and Jens Reeder(@jensreeder).
Logo
scikit-bio's logo was created by Alina Prassas.
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Category: | General |
Publisher: | Basic Integrated Software |
Last Updated: | 01/23/2019 |
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License: | Freeware |
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