immunarch

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A very large number of BCT clone type abundance

3

When I run the following code to explore the number of clone type for each sample `exp_cnt

zh-zhang1984

Issues with repDiversity

2

I've been using repDiversity and noticed several issues, which I'm putting all here together for simplicity: # documentation issues 1) .max.q default is actually 6, not 5: ``` .max.q |...

fabio-t

Bcell lineage analysis

7

## 🚀 Feature Allow plotting of "clonal trees" for bcell data, rooted on the germline. ## Motivation B-cell repertoires are interesting because of SHM - you can group together different...

fabio-t

rarefaction analyses and sampling depth

1

hello thank you for all these great tools. would it be possible to generate rarefaction curve to assess sampling depth (e.g. by subsampling data without replacement at XXX sequence increments,...

antoine4ucsd

import directly from seurat object

4

Hi! I was hoping you can provide some guidance on importing processed Seurat objects (that contains the metadata) directly into immunarch for exploration. I tried importing the .txt count matrices...

wfma

calculating Morisita index isn't working

1

Hi! I am facing an issue while trying to calculate repertoire overlap, Morisita index in particular. Not sure whether this is truly a typo/a bug and not myself doing something...

AnnaVyborova

Add Shannon-Wiener index in repDiversity

7

## ❓ Questions and Help I added Shannon-Wiener index in my repo https://github.com/wangshun1121/immunarch/blob/master/R/diversity.R usage: ``` div = repDiversity(immdata$data, "shannon") ``` I think Shannon-Wiener index should be included!

wangshun1121

## ❓ Questions and Help We have a set of [listed tutorials available on the website](https://immunarch.com/articles/).

deepakphd

Discrepant results for vloupe

2

Hi, First please let me state this is a fantastic package and I have throughly enjoyed learning how to use it! I'm having some issues with discrepant results when loading...

JFavaloro

spectratpying

1

Concerning spectratpying, is there a way to change the axes (particularly the y-axis)? I would like to keep the axes the same for all my spectratype plots.

jvelazquez14