Qiyun Zhu

As @wasade and I noticed, scikit-bio at Bioconda is as old as 0.5.6. We may consider providing support for an updated Bioconda recipe.

Efficient sequence alignment path data structure

1

### Discussed in https://github.com/scikit-bio/scikit-bio/discussions/1973 @mortonjt @wasade Will appreciate your thoughts! Originally posted by **qiyunzhu** March 17, 2024 Here I am describing the plan to implement a multiple and pairwise sequence...

This issue documents the procedures of testing skbio against QIIME 2 to see if anything may break. The procedures follow the QIIME 2 [development documentation](https://dev.qiime2.org/latest/quickstart/). @wasade @mortonjt @mataton Create a...

WIP Elevating skbio.stats.xxx to 1st-level modules

1

This PR elevates `skbio.stats.xxx` to 1st-level modules. Such that a user can do `from skbio.composition import ancom`. Whereas the original entries are kept for backward compatibility. This PR also standardizes...

Add more zero replacement methods

1

I came across the very long function name [`multiplicative_replacement`](https://scikit.bio/docs/dev/generated/skbio.stats.composition.multiplicative_replacement.html). Then I started to think if there are things we can add. This article: [Comparison of zero replacement strategies for compositional...

Lots of changes are being made since skbio 0.5.9. This issues records changes that might break or alter the behavior of QIIME 2 (q2). The skbio team will work the...

There is a nice text art in `skbio/__init__.py`, which represents a basic tree of life: ``` Opisthokonta \ Amoebozoa \ / * Euryarchaeota \ |_ Crenarchaeota \ * \ /...

It says: ```scikit-bio does not currently support translation of degenerate sequences.`RNA.expand_degenerates` can be used to obtain all definite versions of a degenerate sequence.``` It shouldn't be hard to implement degenerate...

The current scikit-bio codebase has several plotting functions, such as heat map for `DistanceMatrix` and scatter plot for `OrdinationResults`. However, the way the plots are delivered may be outdated. Take...

Update: Using NumPy's new random generator ([NEP 19](https://numpy.org/neps/nep-0019-rng-policy.html)) improves performance by 10 fold. This is because the new [`numpy.random.Generator.choice`](https://numpy.org/doc/stable/reference/random/generated/numpy.random.Generator.choice.html) uses the [Floyd's algorithm](https://dl.acm.org/doi/10.1145/30401.315746) to accelerate sampling speed, especially when sample...