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The [qiime_test_data](https://github.com/qiime/qiime_test_data) repository is currently separate from QIIME. I think it'd be a good idea to merge it into the QIIME repository, as this will help sync u…
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@antgonza brought up a good point:
For the alpha rarefaction/boxplots text, should the text include explanations for chao1 and shannon (in addition to observed species and PD)? These are the four alp…
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All explanatory text (e.g. alpha rarefaction, beta diversity, etc), as well as the content that will go in the emails, needs to be reviewed and modified as necessary before we push out the delivery.
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In addition to the per-student index pages, we should have a top-level index page for the website that contains information about the project, the delivery system, and anything else we want to put in …
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Specifically, line 130:
https://github.com/qiime/qiime/blob/master/qiime/alpha_diversity.py#L130
Thanks @antgonza for highlighting this problem. The underlying issue is two-fold. First, the `iterSam…
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Assess similarities between different time trajectories across body-sites or even across individuals.
The idea here is to be able to find _signals_, where the `x-axis` is time and the `y/z-axes` are …
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i think this order: taxa area plots (self v other); PCoA; alpha diversity box plots at 10k sequences; otu category significance tables; alpha rarefaction plots
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A boxplot would probably be good here showing, on a per-body-site basis, other (in a box) with self as a single point next to the box. This might involve some custom code, but @jrrideout is the box-pl…
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In biom-format/python-code/biom/**init**.py, lines 53 and 54:
```
if backend is None:
backend = 'SparseDict'
```
this should be
```
if backend is None:
backend = 'SparseMat'
```
otherwise …
cleme updated
11 years ago
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integrate test set from `qiime.test.get_test_data()` and `qiime.test.get_test_data_fps()` in all workflow tests to facilitate faster runtime and improved features of this test set (see #582 for discus…