So excited to see this publication finally come out. This was my first project I worked on with the Karnes Lab and I really think it became a diamond from the rough.
Significance Skyline with Manhattan Plots Manhattan plots are a type of scatter plot that show the statistical significance of a genomic variant with an outcome of interest. Yan Holtz made a self-annotating manhattan plot for the R Graph Gallery.
The best way to improve prediction is to increase the amount of data you’re using to do the prediction. With warfarin, the anticoagulant I study, there are limited sources of explored variability in drug response.
Qiime My sequencing was done by Ion Torrent which made Qiime a bit difficult to use because of lacking documentation. I followed, mostly, this post by Carli Jones: https://forum.qiime2.org/t/possible-analysis-pipeline-for-ion-torrent-16s-metagenomics-kit-data-in-qiime2/13476.