hammerlab/immune-infiltrate-explorations

Name for this project/tool

Opened this issue · 6 comments

jburos commented

Creating this issue to keep track of random ideas for project name

@maximz :

something simple like "infiltrate" or "infiltration" could work, or maybe a quasi-synonym like "percolate"

Some other ideas:

  • TypeSeq
  • Immuno
  • imax
  • aceso: who is apparently the goddess of the process of healing
  • MCMSeq

An open question is whether to emphasize "immune" in the process or brand this a more generic infiltrate / cell type deconvolution algo

hammer commented

Ooh aceso is a good one to keep in mind but not for this project. What about something direct like UnmixRNA?

maximz commented

Thank you all for the suggestions above -- this is great.

I worry that TypeSeq and MCMSeq sound like sequencing technologies, UnmixRNA sounds a lot like the existing tool DeconRNASeq, Immuno is a bit broad, and imax will be tough for SEO. If I'm misjudging these, let me know.

I wanted to throw some more ideas into the mix:

  • hierosort / hieroseq: using hierarchy to sort sequencing data
  • split or immunosplit: SeParate lines of immune/infilrate types
  • sift or immunosift: separate immune inFiltrate types
  • (immunosort seems to be a real technique?)

Thoughts on these?

Some other options, though the trouble with these is search engine rankings are problematic for common words and misspellings:

  • bait: Bayesian analysis of infiltrate in tumors
  • beast: Bayesian extraction and sorting for tumors
  • gembit: gene expression mixture Bayesian immune typing
  • mixtape: a play off mix-type and the music theme we have at hammerlab (e.g. epidisco)
  • supertype: superclass typing
  • debt: deconvolve expression with Bayesian typing
  • debit: deconvolve expression with Bayesian immune typing
  • bild: Bayesian immune lineage deconvolution

If anything is jumping out for you above, would love to hear about it. Otherwise I will keep iterating.

Relevant keywords if anyone else at hammerlab wants to give this a shot:

sort, extract, hierarchy, (immune) infiltrate, (immune) cell, lineage, bayesian, generative, rna-seq, deconvolve, mixture, expression, transcript, count, cancer, tumor, microenvironment

Existing tool/approach names we should stay away from:

xcell, cibersort, precog, decon-rnaseq, estimate, immunoscore

maximz commented

mixtape received some votes. Some other proposals:

  • unmixtape
  • TIL-type
jburos commented

Just to throw some other ideas out there, I've been thinking along the lines of inference - infertype, type-inference, infermix. or, using the "-hat" moniker, ala yhat: "typehat" (going free association: tophat, hattrick, .. etc )

maximz commented

Thanks @jburos ! I like this Bayesian inference of immune infiltrates idea.

Jumping off that, here's one more: infil-traits, infer-traits, or infertrate: infer traits of immune infiltrates

maximz commented

inpheno: infer the distinguishing traits of expression phenotypes

One reason I like this name is it broadens the discussion. The tool is not limited to the immune infiltrate use case -- phenotype differentiation is useful elsewhere in immunology, and generally in biology. Also, I think users don't care how our tool works. The point for users isn't that we've made an incremental improvement to deconvolution tools by using hierarchy and adding RNA-seq support, but rather that this is a broadly usable Bayesian inference tool for differentiating expression phenotypes.

Or infino: infer infiltrate phenotypes

And a suggestion from Cindy: inpherno

This is pushing it, but: inpheRNA