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

fix build badge

Travis removed, but GHA is erroring for not finding waldronlab/omicidxClientR

Create function to add ontology columns to metadata table

This is an orphaned enhancement item.

create "recommended" option for requiredness in template.csv

@paolinomanghi @edoardopasolli where should there be a "warning" option in the template? If it is added we can use it.

create "recommended" option for requiredness in template.csv

Call this "recommended" instead.

Simplified methylation data

Thanks for the code, @pcheng84! Yes it would be convenient to have a simplified methylation version pre-computed. @LiNk-NY, it looks like the `c("REF", "Chr", "Loc", "Island", "Gene", "UCSC_RefGene_Group")` (and possibly...

Viewing Clinical Data Floods Console With Text

I actually discussed this with @vjcitn recently - I think the gist of our conversation was that `DataFrame` itself could use a better show method for when there are lots...

converting Mutations components to maftools-friendly form?

Couple thoughts: 1. A MAF-like form wouldn't be compatible with MultiAssayExperiment, so a coercion method to DataFrame probably would belong with the RaggedExperiment package. 2. It is a pain to...

converting Mutations components to maftools-friendly form?

The gist now converts the RaggedExperiments to RangedSummarizedExperiments, instead of matrices.

converting Mutations components to maftools-friendly form?

Back to my comment 1 - this coercion method could be useful for GRangesList as well as for RaggedExperiment, so it's not even just a RaggedExperiment question.

converting Mutations components to maftools-friendly form?

@vjcitn and @LiNk-NY take a look at the [conveniencefuns](https://github.com/waldronlab/curatedTCGAData/tree/conveniencefuns) branch I just pushed. It's far from perfect but does the following: ``` > accmae accmae A MultiAssayExperiment object of 4...