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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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Where can I find the barcode for single cell identify from the returned object of repLoad ? #164

Open zh-zhang1984 opened 3 years ago

zh-zhang1984 commented 3 years ago

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 commented 2 years ago

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 support@immunomind.io.

Best regards, Immunarch team