scikit-bio-cookbook

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recipe for visualizing within vs between distances

2

@gregcaporaso and I were chatting (offline and in https://github.com/biocore/scikit-bio/issues/764) about adding a recipe showing how to visualize "within" vs "between" distances using scikit-bio (`DistanceMatrix`), pandas, and seaborn's boxplots. This recipe...

jairideout

recipe illustrating visualizing a BIOM table with seaborn heatmaps

1

See [here](http://stanford.edu/~mwaskom/software/seaborn/examples/structured_heatmap.html#structured-heatmap). This depends on porting the biom table to skbio.

gregcaporaso

gregcaporaso

new recipe illustrating power analysis (possibly with microbiome data)

5

Depends on skbio's [#636](https://github.com/biocore/scikit-bio/pull/636).

gregcaporaso

add recipe to test for association between some phenotype and phylogeny

4

For example, we could look for associations between the geographic distribution of viruses and phylogeny. This could be done by computing euclidean distances between where (geographically) a particular viral strain...

gregcaporaso

add recipe on using normalized mutual information for RNA secondary structure prediction

3

This could take as input an alignment of functional RNA molecule sequences, and output a matrix of mutual information scores for all pairs of positions in the alignment. That matrix...

gregcaporaso