DEICODE
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biocore
Robust Aitchison PCA from sparse count data
I am receiving a "segmentation fault" error when I try to run DEICODE auto-rpca. I've tried running it both in QIIME2 and standalone, with the standalone as the most recent...
Hello! First of all, thank you for clearly addressing the issue of compositionality and the high probability of artifacts in ordination methodology. I wanted to ask if there would be...
Hey @gregcaporaso I wanted to ask if all DEICODE transformed data meet the main assumption for PERMANOVA? [https://stackoverflow.com/questions/35410860/permanova-multivariate-spread-among-groups-is-not-similar-to-variance-homogeneit] I tested it on my data after DEICODE transformation. Only some datasets...
I am new to microbiome data analysis I am trying to use DEICODE to generate distance matrix. Is there way to convert otu_table generated by R and dada2 pipeline otu_table...
Hello, I previously left a comment about having issues with arrow bias in the deicode biplot (scher-lab #56). The recommendation was to re-install with the dev version, which I did....
Some users would benefit from being able to access the rclr transformed values, including myself. I wrote this quick addition to return the rclr matrix and print it as tsv....
Wanted to pull up the paper and disappointed it wasn't in the README! https://msystems.asm.org/content/4/1/e00016-19
I'm trying to use `U,s,V = OptSpace().fit_transform(A_)` but there are no defaults for `OptSpace` and there is also no `fit_transform` method. How can I use your `DEICODE` Python package without...
Is it possible to condense (or collapse) the deicode distance-matrix back into features but keeping the log-ratio transformations and matrix-filling? As for any of the downstream phylogenetic analysis, the functions...
I think there might still need to be some changes made regarding parameter names (since it looks like `--rank` has been changed to `--n_components`, and `--iterations` has been changed to...
