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).
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!