immunarch

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Different samples have different sequencing depth. So, a sample with more sequencing data may show more clonaltypes or higher diversity. Is this factor considered in the Chao1 calculation?

chjp

Problem generating mds plot after repOverlap

10

## 🐛 Bug Hi There, I am running into an error while trying to graph with vis after repOverlap, exactly as detailed in the manual ## To Reproduce Steps to...

peter-yufan-zeng

circos plot or matrix reporting combinatorial usage of V and J chains (D?)

2

## 🚀 Feature a function producing matrices or circos plot for a given sample with the different V-J combinations as edges and number of clones/reads as weight as done in...

splaisan

Parser for RTCR

3

https://github.com/uubram/RTCR

vadimnazarov

## 🐛 Bug "Plot to R console" does not seem to bring the resulting code back to the RStudio Rscript ## To Reproduce Steps to reproduce the behavior: 1. open...

splaisan

ENH: Improvement to trackClonotypes

5

## 🚀 Feature Improvement to trackClonotypes(...) ## Motivation ## Pitch ## Alternatives ## Additional context Currently, we have an initial tech spec for the function, that allows to start coding...

EugeneRumynskiy

top() lacks the "unique" functionality

2

Hi Dr. Nazarov I found another bug, may not a bug? Could please help check? When I use the top() function, I set ".n" = 50, however, in some sample,...

decenwang

pubRepFilter: Use .by to filter by multiple parameters

2

I need to stratify my dataset by multiple parameters with multiple variations with pubRepFilter: pr.clonotypes

k-blenman

## 🚀 Feature Parsing for the PyIR format https://github.com/crowelab/PyIR

vadimnazarov

Suggestions: Include a Chao-Jaccard abundance index function for repOverlap

1

https://github.com/immunomind/immunarch/blob/9dce2ea78f4fb15557e17664910f14c47caa8e63/R/overlap.R#L222Anne The formula for the Jaccard index (though it might technically be a coefficient) used is a comparison of sequence occurrence, regardless of how often it appears in the set...

abrown435