Q2-perc-norm community plugin


(Claire Duvallet) #1

Hi everyone,

Our method to percentile normalize data to allow for pooling data across different datasets has a first working plugin, q2-perc-norm! You can read more about the method at our Plos Comp Bio paper.

The plugin lives on github for now: https://github.com/cduvallet/q2-perc-norm. To install it, clone the directory and run python setup.py install from within the q2-perc-norm directory. (Make sure you’re in the qiime 2 environment or else this won’t work). I’ll be working to make this conda installable in the next few weeks.

A note that the output of the percentile-normalize method is an artifact of type FeatureTable[PercentileNormalized], which is currently not an allowed input to any QIIME 2 functions! I’ll be going through the core QIIME 2 code in the next few weeks and making sure that the functions which are applicable to percentile normalized data recognize this artifact type. For now, however, you’ll need to export the output into a text file and either re-import it as a different kind of FeatureTable or just use it in non-QIIME downstream analyses (e.g. python or R).

Big thanks to @ebolyen and @thermokarst for your help throughout the development process!

Let me know if you run into issues or have ideas for improvements, either in this forum or by raising an issue on the github. Thanks!

Batch Correction - Dealing With Negative Values for Diversity Analysis
(Claire Duvallet) #2

The plugin is now on conda! To install with conda, run:

conda install -c cduvallet q2_perc_norm 

Note that you need to have QIIME release 2018.4 or later for the plugin to work, and that you need to be in the QIIME 2 environment before calling this.

(Matthew Ryan Dillon) #3

5 off-topic replies have been split into a new topic: Q2-perc-norm - ImportError: cannot import name ‘PercentileNormalized’

Please keep replies on-topic in the future.