propr
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tpq
An R package to calculate proportionality between vectors of compositional data
Hi, thanks for your great work. Considering many single-cell methods are developed also in python, I wonder if you have plan to extend your design to Python platform. Thanks a...
Hi @tpq ! While running propr using an older version (v4.0.0), I found that for some datasets different coefficients were obtained in comparison to the latest propr version. May I...
A colleague of mine asked me why use proportionality when they could instead use CLR transformation followed by Pearson/spearman/biweight midcorrelation. I vaguely remember reading why this isn't compositionally-valid but I...
Hi there! First off, thanks for such an awesome package. Second, I was hoping for some help integrating it into a complex study analysis I'm doing. It involves microbiome and...
I am trying to use both the propr and alex2 packages, but am getting errors with the aldex.glm function because depending on which package took precedence in loading it is...
I finally got my hands on a dataset with properly designed ERCC92 spike ins. The question is, how should I use these with ALR in theory? > The additive log-ratio...
From e-mail: >I have tried using the lr2cor function which appears to work well. I would just like to check that I am interpreting the results properly, as I am...
Hi Thom, I remember listening to your bioformatics chat podcast (https://bioinformatics.chat/propr) a while back and recently dove into the literature on several compositional data analysis reviews/methods/papers such as https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755255/ and...
Thanks and regards as ever to the devs. I'm considering several sets of 'omic data generated from the same cohort of ```FASTQ``` files (i.e. taxonomic, pathways, etc). The way of...
Hi! I am trying to use propr for a co-occurrence analysis. I noticed that the log-ratio values calculated by propr (data @logratio in the output) sometimes are quite different with...
