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Hi there,
Congrats on a great work, and thanks for developing this package.
I am attempting to pull TCR-seq data for T cells that also have the GEX/CITE-seq Seurat objects.
**QUESTION 1.** …
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I hope you're doing well. I recently came across your paper, 'TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data,' published in Nature Methods. I was highly impressed by t…
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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 sin…
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Hi,
I am trying to get the hill number, but it requires the error bar parameter file.
To generate the error bar parameter file, I will need a directory which has all the error bar fitting file.
Ho…
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Hello
we have an app wrapped for immune arch on DNAnexus and consistently are getting this error for many sample types and it looks like the tSNE plot doesn't like the data upstream and is throwin…
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Both Genotype and MHCGenotype are nested more deeply than typical for the schema. `MHCGenotype.mhc_alleles` and and `Genotype.*_alleles` could be pulled out into top level objects with refs in Genoty…
javh updated
4 months ago
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Since Healthy isn't a disease, there is no DOID entry for it. So you can't say `diagnosis.disease_diagnosis = Healthy`.
It isn't safe to assume that `diagnosis.disease_diagnosis` == null means that…
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When downloading this file ('iatlas-ici-features.tsv') from the Synapse portal it's not given in the description what the meaning of the columns are.
There seem to be columns linked to various stu…
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Hello,
I want to try `imrep` with my RNA-seq data. I've aligned the `fastq` to genome with `STAR`, and saved the unmapped reads in `fastq` format (using `--outReadsUnmapped Fastx`). As you said, `S…
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Comment below with questions or thoughts about the reading for this week's workshop.
Please make your comments by Wednesday 11:59 PM, and upvote at least five of your peers' comments on Thursday pr…