QIIME 2 plugin for percentile normalization to correct for batch effects in microbiome case-control studies.

install guide:

You can install this plugin by cloning this repo and installing manually. (Older versions of the plugin are available on conda, but these are not compatible with pandas >= 2.0). You need to have QIIME 2 version 2018.4 or later.

You should be in a QIIME 2 environment for the installation process. Install QIIME 2 and activate the QIIME 2 virtual environment before installing this plugin.

To install from this repo, clone the repo to your computer, cd into the main directory, and run:

pip install .

You can check that the installation worked by typing qiime on the command line. The perc-norm plugin should show up in the list of available plugins.

q2-perc-norm

QIIME 2 plugin for percentile normalization to correct for batch effects in microbiome case-control studies.

Read more about the method in our paper (Gibbons et al, PLOS Comp Bio 2018).

Tutorial

See the documentation on the git repo for more information on how to use the plugin: https://github.com/cduvallet/q2-perc-norm

Citing

If you use this plugin, please cite:

Sean M. Gibbons, Claire Duvallet, & Eric J. Alm. (2018). Correcting for batch effects in case-control microbiome studies. PLoS computational biology, 14(4), e1006102. doi:10.1371/journal.pcbi.1006102

Need help?

Use the community plugin category in the QIIME 2 forum. Please tag @cduvallet in your post so that it gets to the right person.