vadimnazarov
commented
3 years ago Hello @rcarrr and thank you so much for signing up on GitHub to open an issue, I truly appreciate it!
I'm deeply sorry for the very late response. We've been extremely busy raising investments and hiring the team after finishing UC Berkeley startup accelerator. We are finally set up for now: we grew the team from 4 to 15 amazing professionals, and raised a large investment round from great investors. Thank you so much for your patience!
In order to subset repertoires by the gene of interest you could use dplyr's function filter. The code would look something like this:
immdata$data = lapply(immdata$data, function (x) x %>% filter(V.name == "TRBV4-1") %>% collect())Please let me know if it works for you or if you have other use cases in mind.
Improving upon Immunarch, we will soon release our online analytics platform for fast, effortless and code-less reproduction of impactul single-cell transcriptomics and immune repertoire publications. It's designed for researchers who spend a lot of time or energy reproducing sophisticated pipelines or analysing datasets from publications. Feel free to send us a link to publications of your interest so we can reproduce them on our platform and give you an access.
We are more than happy to grant you an early access as our gratitude for you being a longstanding immunarch user.
We have a list of datasets from around 30 publications that we are going to make available for your exploration and analysis. As an example, we recently reproduced on a platform a paper focused on scRNAseq-based estimation of efficacy of CAR-T immunotherapy.
Please send links to support@immunomind.io. The direct link to the publication datasets would be also greatly appreciated.
Hi, I'm using immunarch on a set of 3 cell types (2 biological replicates for each one). I was wondering if there is the possibility to perform all the steps (repOverlap, repDiversity,...) on a single gene (i.e. only on TRAV or TRAJ genes) and not in the total combination. Is there the possibility to consider the output of geneUsage to this aim?
Thank you in advance!