-
Hello,
I am running ppanggolin on about 40K species, on a slurm managed cluster, and after some time the multi-threaded processes hang indefinitely.
My initial thinking was that the total memory …
-
Hi,
I saw your q2-repeat-rarefy qiime2 plugin and really appreciate your contribution to the microbiome community.
However, I think the idea of multiple rarefaction is incorrect from a statistical p…
-
As described in Chao et al.
Their web application iNEXT-PD / PhD and the bird data demonstration of their formulae differ from our use cases in some respects:
1. We have separate phylogenetic tr…
-
**Improvement Description**
Save the shown plots e.g. from `qiime diversity alpha-rarefaction` additional as SVG/PNG/whatever as it is possible in `qiime taxa barplot`
**Current Behavior**
One c…
-
**Improvement Description**
The new `alpha-rarefaction` visualizer @maxvonhippel authored is almost ready for merge (#128) and will be included in the 2017.8 release! :tada:
When reviewing #128 I…
-
When I run multiple_rarefactions with -m 1, then later on in the pipeline, the plotting is giving me errors (I suspect it's because of this). When I reran the whole pipeline with -m 100, it was fine. …
-
Hey guy,
The -e (MAX_RARE_DEPTH) in alpha_rarefaction.py used median as default. Can we add "-e max" to set the -e to the maximum. Otherwise, we need to figure out what's the exact maximum number and…
-
- [x] update app to work with mobr dev branch (which will be merged soon into master as mobr v2.0 is rolled out)
- [x] some of the arguments to `make_mob_in` and `get_delta_stats` have changed
…
-
## 🐛 Bug
The generation of rarefaction curves using the `repDiversity` function with the option `.method = 'raref'` seems to work fine with a few datasets that I have tried. However, when I try to vi…
-
**Describe the Bug**
When I use mStat_normalize_data() with the Rarefy-TSS method, the mStat_validate_data() function no longer passes because it doesn't recognize feature.tab as a matrix (Rule 5). W…