immunarch

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Other supported formats

2

Hi, can immunarch read in repertoire data that has been outputted from the CLC Workbench from Qiagen (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-main-workbench/)? Repertoire data is outputted in the format of .txt files which should...

robwatson15

paired data issue

5

Hey everyone. I am trying to use this tutorial (https://immunarch.com/articles/web_only/v21_singlecell.html) in order to load my 10x TCR data in order to track clonotypes across seurat clusters (as shown at the...

christoforos-dimitropoulos

repFilter function not found

1

Hi, I am new to using immunarch. I would like filter my data by removal of least abundant (rare) clones with frequency of 0-5. I am trying to do it...

venlag

Integration with Seurat and barcode names

3

Hi love Immunarch! Such a great tool. I have been using it for the analysis of clusters of B cells analysed through Seurat but when I use integrated anchoring in...

aleofifi

About calculating Diversity

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## ❓ Questions and Help We have a set of [listed tutorials available on the website](https://immunarch.com/articles/). Hi, When I try to use your package to calculate diversity of T cells,...

Qlinsane1

Plots from large datasets are congested

4

I'm testing immunarch in a jupyter notebook for use in an upcoming project. The plots look great when the sample count is small. However, when it gets into the hundreds...

jakewendt

Exp_clones in bulk data

3

## ❓ Questions and Help We have a set of [listed tutorials available on the website](https://immunarch.com/articles/). I was wondering how the number of clones is calculated for bulk data. My...

licmn

Error in library(immunarch) : there is no package called ‘immunarch’

2

Installing 'immunarch' ... [1/7] Installing factoextra... Installing package into ‘/Users/rmahla-admin/Library/R/x86_64/4.1/library’ (as ‘lib’ is unspecified) Warning: unable to access index for repository https://cran.rstudio.com/src/contrib: cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES' Warning: unable to access...

mahlaranjeet

Error in strsplit(df[[.dalignments]], "|", TRUE, FALSE, TRUE)

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## 🐛 Bug I get this error when I use repLoad(/path/to/mixcrclonesoutputfile.txt). Error in strsplit(df[[.dalignments]], "|", TRUE, FALSE, TRUE) : non-character argument I recheck the data and find the error arise...

chenyx47

Support to repLoad the clone files generated by Trust4 program.

5

## 🚀 Feature Support to repLoad the clone files generated by Trust4 program. ## Motivation Among the clonotype identification tools, Trust4 is an emerging tool that are recently updated. Its...

sciencepeak