SRS as a normalisation method.

Developer Discussion
1

Hi team

I am interested to add SRS as a plug-in in qiime2 and would be appreciated if you could give me some guidance of how I can implement this as a plug-in in qiime2?

Thanks in advance
Marwa

2

Hi @MarwaTawfik,

Not to discourage you, but have you seen q2-SRS?

https://library.qiime2.org/plugins/q2-srs/31/

Best,
Justine

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That is not discouraging, I just don't want to use rarefaction but SRS instead. Thanks for sharing this. I have been using nf-core/ampliseq so they haven't incorporated this yet. Do you contribute too to nf-core/ampliseq upgrades? as they are currenlty only using rarefaction option from qiime2.

4

Here is my thread awhile ago, regarding this.
Could you please help with the container part?

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I had a short look and found that SRS has an R package and is in conda-forge, see R Srs | Anaconda.org, but I could not find a docker or singularity container, which is a prerequisite to integrate it (might have missed it, also possible to create own container ofc).
It also doesnt seem to be in any QIIME2 container, see Index of /qiime2/

1 Like
5

Hi @MarwaTawfik,
Have you looked at this post? It discusses how to install an r package in our docker image: Install phyloseq in qiime2 docker container - #7 by thermokarst

Hope this helps!
:turtle:

2 Likes
6

Hi @MarwaTawfik, You can also check out Developing with QIIME 2 for general information on creating QIIME 2 plugins, in case that is helpful for you. We should have a how-to article in there shortly that illustrates how to wrap R code in a QIIME 2 plugin. You can track progress on that here.

1 Like