Sidney Bell
Sidney Bell
I think it's important to contextualize diffexp results by what these genes _do_, biologically. There are multiple "levels" at which we could support this: 1) Just link out to wikigene...
From @aopisco: If a user creates a cell type annotation as in #996, allow them to link each label to a specified `gene set` as evidence (with congruent, ontology-based names...
**Context** The ability to subsample using a `focal` set and then background context selected by genetic relatedness is SUPER useful. We'd like to be able to do this for other...
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### Description of proposed changes Documents how to parse nextstrain JSON files to a common library for downstream phylogenetic analysis. I suspect this is code that is being reinvented by...
E.g., I'm currently writing a couple of functions to take the auspice tree JSON and import it into a notebook as an ETE toolkit Tree object. If this seems helpful...
### Current Behavior ### Expected behavior The current layout code for calculating the (x,y) coordinates for the unrooted layout is deterministic, and doesn't include any sort of offset for showing...
Expected: `some **bold** text` --> some **bold** text Observed: * `some **bold** text` --> `some **bold** text` * ` some **bold** text` --> `some **bold** text` * ` some bold...
**Context** One of the things that makes trees really intimidating to non-phylogeneticists is all the really deep branches / nodes. While these deep divergence events are super helpful for us...
**Context** Example use case / job story 1: "when I am looking at an outbreak cluster, I want to copy the names of closely related samples so I can go...