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Hi Joey,
I started using phyloseq last November and am so glad to have the package for managing my microbial sequence data. Recently when I downloaded another package with various dependencies, I wa…
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Hello,
A few weeks ago I was running DESeq2 and then using the tutorial here:
https://github.com/joey711/phyloseq/issues/283
to make a heatmap of the variance stabilized data.
I updated my version…
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When sorting a table that has been filtered so that it is empty (0x0), an uninformative error message is raised. This only seems to happen if the table is filtered to be empty; creating an empty `Tabl…
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Trying to load an empty file, yields a rather non-informattive error, it would be really nice if a more informative error was raised instead, though I understand if this is out of the scope of the par…
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I'm a terrible human being for not having this out yet.
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The `fork me` ribbon doesn't work very well when the window is resized, see #389.
@ElBrogrammer volunteered to fix this in a later pull request.
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(from Se Jin and LukeU) Currently, there is no easy way to decide on rarefaction level so add a summary/histogram of seqs/samples before selecting parameters for analyses.
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When running `print_qiime_config.py` against the latest dev versions of QIIME and biom-format:
``` bash
$ print_qiime_config.py
Traceback (most recent call last):
File "/home/jrideout/.virtualenvs…
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tests/test_rarefaction.py fails with biom-format 2.1.3 and h5py:
```
$ python tests/test_rarefaction.py
.....F
======================================================================
FAIL: test_rarefy…