B. Arman Aksoy

(assigned myself on purpose to improve my ketrew skills a bit ;))

@etheleon: not sure I understand what the problem is here. If you are developing against pileup.js, you might need to `npm install` within pileup to get all those dev packages,...

Thanks for reporting this John! Looks like this has something to do with the sparse matrix implementation that `igraph` uses. I will try to isolate this problem to a test...

Thanks, @nklepeis! This package, unfortunately, is pretty outdated and I won't be able to update it to include this type of a functionality any time soon. I will keep this...

We now have a dedicated public bucket: `gs://cytokit`. Added data sets that are relevant to the manuscript: ``` $ gsutil ls gs://cytokit/datasets/* gs://cytokit/datasets/cellsize/: gs://cytokit/datasets/cellsize/20181024-d38-act-20X-5by5/ gs://cytokit/datasets/cellsize/20181024-d38-unstim-20X-5by5/ gs://cytokit/datasets/cellsize/20181024-d39-act-20x-5by5/ gs://cytokit/datasets/cellsize/20181024-d39-unstim-20x-5by5/ gs://cytokit/datasets/cellsize/20181024-jurkat-20X-5by5/ gs://cytokit/datasets/cellsize/20181024-jurkat2-20X-5by5/ gs://cytokit/datasets/cellsize/20181026-pmel-act-20x-5by5/...

I am planning to work on this week. OK with you @ihodes?

yeah, we also want this for the RCC stuff - so would be great to have this in epidisco to generalize. No promises on a robust QC metric, but I...

Yep! Will be bundling this with the planned QC improvements: https://github.com/hammerlab/biokepi/pull/381

Here is the backstory on this one: Strelka's VCF implementation is not complete and VCF validators fail them because of the weird choice of fields/annotations they use in the VCF....

@jburos: unfortunately there is no silver bullet here: `pyvcf` is pretty robust and is the de facto library for the field so I trust it; but unless you make sure...