Levi Waldron

icon indicating a website link https://waldronlab.io icon indicating an email [email protected]

icon company The @waldronlab at the City University of New York icon location New York, NY icon location I teach biostatistics, develop for Bioconductor, and have an active research program in cancer genomics and in metagenomic profiling of the human microbiome.

Results 90 comments of Levi Waldron

Make this run faster

As Jenny Bryan would say, it has a bad code "smell"

Clarify what `blockCol` is

By the way, I noted that the original Python LEfSe functions and manuscript refer to "class" and "subclass", not "group" and "block" (e.g. https://huttenhower.sph.harvard.edu/lefse/ for galaxy module and https://github.com/SegataLab/lefse/blob/master/lefse/lefse_run.py for...

support multigroup

@shbrief don't forget this PR!

support multigroup

@sdgamboa (and maybe @asyakhl ?) would you take a look at this PR and think about the plotting of multiple classes? I think it would just mean multiple pairwise classic...

support multigroup

@asyakhl reminder of this pull request to review.

NAs and identical pvalues in annotateRAV

Thanks! A raw p-value cutoff, or a qvalue cutoff? It's surprising that with hundreds of gene sets, none would have even a raw p-value < 0.05. Also, are you sure...

Documentation and user control over PCA

FYI @helenalc in case you have anything to add

returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType

Thank you for the report, and I'm terribly sorry for the delay. @schifferl I can reproduce this bug, it seems to be an invalid replacement of the assay in a...

Offline validator functionality

@krlong68 I just tried installing and running the vignette from the [metadata-validator branch](https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/metadata-validator) - I see an error `Error in FUN(X[[i]], ...): object 'ok' not found` but it does seem...

## MetaCardis2020a gene_families data cannot be retrieved, even with high memory

I also can't reproduce this error in Bioconductor 3.21. I wonder if you have some version mismatch, because ExperimentHub database pointers can point to different resources in different versions. Could...