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scikit-bio

@scikitbio
scikit-bio.org
Joined April 2015
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  • Followers199
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scikit-bio retweeted
Qiyun Zhu (@zhuqiyun) profile picture
Qiyun Zhu
@zhuqiyun11 Dec 2025
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. nature.com/articles/s41592-0… #Bioinformatics #OpenSource
Scikit-bio: a fundamental Python library for biological omic data analysis

Scikit-bio: a fundamental Python library for biological omic data analysis

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

nature.com
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scikit-bio 0.6.3 is out! Featuring a massively upgraded tree and phylogenetics module, with scalable algorithms for tree building, refinement, comparison and manipulation, plus improved file I/O and random seed. github.com/scikit-bio/scikit… #Bioinformatics #OpenScience #Microbiome
Release scikit-bio 0.6.3 · scikit-bio/scikit-bio

Release scikit-bio 0.6.3 · scikit-bio/scikit-bio

We are excited to announce scikit-bio 0.6.3! This is a massive upgrade, despite minor version change. Release highlights include: Significantly improved the tree and phylogenetics module (skbio.tr...

github.com
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scikit-bio now offers an expanded and well-documented array of alpha diversity metrics, including new generalized and phylogenetic ones like abundance-weighted PD, Hill numbers, and Renyi entropy. scikit.bio/docs/latest/gener… #bioinformatics #microbiome #ecology
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scikit-bio 0.6.2 is out! Windows support (now official), more efficient and capable phylogenetic tree, advanced alpha diversity calculation, and more! Ready for #ISMB 2024. #Bioinformatics #OpenScience github.com/scikit-bio/scikit…
Release scikit-bio 0.6.2 · scikit-bio/scikit-bio

Release scikit-bio 0.6.2 · scikit-bio/scikit-bio

We are excited to announce scikit-bio 0.6.2! Release highlights: scikit-bio now has full support for Microsoft Windows. Significantly improved the efficiency and functionality of TreeNode for stor...

github.com
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scikit-bio now fully supports Windows! Many appreciations to the team's heroic efforts. This is finally in. github.com/scikit-bio/scikit… Stay tuned for the upcoming 0.6.2 release which ships this!
WIP: Full windows support by mataton · Pull Request #2071 · scikit-bio/scikit-bio

WIP: Full windows support by mataton · Pull Request #2071 · scikit-bio/scikit-bio

This PR will update the CI and other necessary elements to enable the use of skbio on Windows machines. Please complete the following checklist: I have read the contribution guidelines. I hav...

github.com
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We are excited to announce scikit-bio 0.6.1! NumPy 2 support, sequence embedding structure for working with language models, efficient alignment path structure, much faster count subsampling algorithm, expanded community diversity metrics, and more! #Bioinformatics #OpenScience
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scikit-bio 0.6.0 is released! scikit.bio New website, new data table module, sample metadata object, diversity metrics and differential abundance test, Python 3.12 support, and much more. #Bioinformatics #OpenScience
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scikit-bio is back in action! scikit.bio Thanks to funding from DOE and a reassembled team. Get ready for: Streamlined analysis of massive omic data, Advanced multi-omic integration, Enhanced biological feature annotation. Join us to advance reproducible #openscience
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We’re excited to announce scikit-bio 0.5.7 has been released, which includes performance improvements and tentative Apple M1 support! Please see github.com/biocore/scikit-bi… for specific changes
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scikit-bio 0.5.2 is now live with support for the EMBL and GFF parsing! github.com/biocore/scikit-bi…
Release scikit-bio 0.5.2 bug fixes and support for EMBL file format · scikit-bio/scikit-bio

Release scikit-bio 0.5.2 bug fixes and support for EMBL file format · scikit-bio/scikit-bio

We're very excited to announce scikit-bio 0.5.2. You can review the CHANGELOG.md for a complete description of the changes in this release. To learn about what you can do with scikit-bio, you s...

github.com
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scikit-bio retweeted
QIIME 2 (@qiime2) profile picture
QIIME 2@qiime29 Feb 2017
#QIIME2 2017.2 is live! Improved DADA2 perf., expanded docs, and new interactive viz! #microbiome #bioinformatics forum.qiime2.org/t/qiime-2-2…

QIIME 2 2017.2 release is now live!

Hi all, The QIIME 2 2017.2 release is now live! You can find the full release notes here, but here are a few of the highlights: Support for paired end read analysis. Parallel processing support and...

forum.qiime2.org
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scikit-bio 0.5.1 is live: support for interval metadata! github.com/biocore/scikit-bi…
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scikit-bio retweeted
QIIME 2 (@qiime2) profile picture
QIIME 2@qiime27 Nov 2016
#qiime 2.0.6 is live, new tutorials and forum! spring 2017 workshop announcement soon. #microbiome #bioinformatics github.com/qiime2/qiime2/rel…
Release qiime 2.0.6: data provenance, simplified viewing, and new forum · rachis-org/rachis

Release qiime 2.0.6: data provenance, simplified viewing, and new forum · rachis-org/rachis

We're excited to announce the 2.0.6 minor release of the QIIME 2 framework and supporting plugins. This is the second synchronized release, meaning that we intend all interfaces and plugins ver...

github.com
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With greater accessibility of #machinelearning, we can experiment with more uses in #marketing. @scikitbio hbr.org/2016/10/machine-lear…
Machine Learning Is No Longer Just for Experts

Machine Learning Is No Longer Just for Experts

You don’t need a PhD, and that’s a big deal.

hbr.org
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0.5.0 is live: first Python 3 only release! github.com/biocore/scikit-bi…
Release scikit-bio 0.5.0: Python 3 only release · scikit-bio/scikit-bio

Release scikit-bio 0.5.0: Python 3 only release · scikit-bio/scikit-bio

We're very excited to announce scikit-bio 0.5.0. scikit-bio is no longer compatible with Python 2. scikit-bio is compatible with Python 3.4 and later. This is a maintenance release containing a...

github.com
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scikit-bio retweeted
QIIME 2 (@qiime2) profile picture
QIIME 2@qiime214 Apr 2016
it's official: QIIME 2 is @NSF funded! nsf.gov/awardsearch/showAwar…
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TIL:pip does not install sdist ending in `-pyX.Y` except on matching Python version: github.com/pypa/pip/issues/3… . Drop Python 2 safely !
Install compatible packages with the Python version being used · Issue #3182 · pypa/pip

Install compatible packages with the Python version being used · Issue #3182 · pypa/pip

(sorry if this issue has been raised before) Recently coverage dropped Python 3.2 support and several PRs of many different projects started failing on travis. Just to make it clear: the PRs were o...

github.com
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