ncborcherding / ibex

Using BCR and expression for sequence embedding

About Me

I am the Head of Computational Biology at Omniscope. I recieved my MD/PhD from the University of Iowa, as part of the medical scientist training program. I was also a member of the Washington University Department of Pathology and Immunology dual residency and post-doc PSTP program. At WashU, I was co-mentored by Jon Brestoff and David DeNardo. My research focused on the use of innate cellular barcodes, such as mitochondrial genome and adaptive immune receptor sequences, to track immune responses and predict clinical outcomes.

More information is available via my website (including pdfs of my publications).

My Google Scholar profile is available here.

GitHub Stats

ibex's Issues

using Ibex when dataset was not processed with scRepertoire

Hello,
this is a great idea, been looking to try something like this and looked like the T cell people were more advanced.

Have a couple of questions:

• I already have an SCE object with integrated vdj data, I have the aa sequences, V gene identity and of course barcode, and I have subsetted so they are all heavy chain only. Is there a way to use this without starting again with scRepertoire?. Looks from getBCR that I could change the name of my colnames in colData for aa, v genes. to match the ones used by scRepertoire.... Would this work? what else would I need to change or make sure to go directly to runIbex with my SCE.

• which dataset was used for the training? Sorry I might have missed it and not very familiar yet with machine learning.

Finally, a suggestion:
Pulling V genes just with grep from GEX data is not ideal as there are a lot of pseudogenes, I would suggest using chromosomal location or the biotype assigned by cellranger, soomething like:
ig_list <- c("IG_C_gene", "IG_C_pseudogene", "IG_D_gene", "IG_D_pseudogene", "IG_J_gene", "IG_LV_gene", "IG_pseudogene", "IG_V_gene", "IG_V_pseudogene")

And then can query into biomart for genes that have that biotype that are also in your dataset.

Carlos

wrong pattern?

Hi, cool repo(s)!

Just a minor thing - wondering if this pattern should be ^IG[HKL][VDJ] instead?

Ibex/R/runIbex.R

Line 86 in 5235eb0

unwanted_genes <- "^IG[HLV][VDJ]"