Where can I find the barcode for single cell identify from the returned object of repLoad ?

[zh-zhang1984]

Hi, thank you so much for the excellent tool for users. I have a question below:

1. I have a single cell immune reportoire data and preprocessed with MixCR
2. loaded by repLoad function.
3. object have the following columns:

> names(immdata$data$`HZ01_d1-B.clonotypes.IGH`)
 [1] "Clones"     "Proportion" "CDR3.nt"    "CDR3.aa"    "V.name"     "D.name"     "J.name"    
 [8] "V.end"      "D.start"    "D.end"      "J.start"    "VJ.ins"     "VD.ins"     "DJ.ins"    
[15] "Sequence" 

The Clones have very large numbers such as:

> summary(immdata$data$`HZ01_d1-B.clonotypes.IGH`$Clones)
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
      1.0       1.0       4.0   37466.6      21.5 2598331.0 

I think this can be the reads number. However, I cannot get the single cell- level data from this dataframe. the barcode identity is not shown in the output. I would like to combine single cell mRNA and TCR data. Is that function supported by the current version?

[MVolobueva]

Hello, @zh-zhang1984 !

Thank you for using our package!

Currently, we are developing a Single-cell support for the Immunarch package.

We have made new tutorial for BCR MIXCR data (https://immunarch.com/articles/web_only/BCRpipeline.html). It may help you.

We will be very pleased and grateful if you consider providng an example of your data. You can send the data directly to our tech support at [email protected].

Best regards, Immunarch team