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🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

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## πŸ› Bug Good Morning, I recently exported immunoSeq TCRB (v4b) data using the Export V2 option and received the following parsing failures. I understand v4b is fairly new and...

tag:IO
status:In progress ⏳
type:Critical

## πŸ› Bug Good Afternoon, I received the following error while using your gene usage function. ``` > imm_gu_cor = geneUsageAnalysis(imm_gu, .method = "cor", .verbose = F) Error: Assigned data...

type:Bug
tag:Methods
status:In progress ⏳

Hi Dr. Nazarov, When I plot by grouping method (.by = "group"), however, there is an unknown group NA existing in my graph. pleas see attached. I checked my metadata,...

type:Bug
tag:Methods
status:In progress ⏳

## πŸ› Bug ``` system.time( immdata

type:Bug
tag:IO
source: Email

## πŸš€ Feature Let repLoad read the clone file that only has the header line. ## Motivation In an experiment of several samples, some samples might have no clones found...

## ❓ Questions and Help Good Afternoon, I was switching to immunarch from tcR. I was missing two things in immunarchΒ΄s geneUsageAnalysis: 1. I was regularly using: `geneUsage(immdata$data, HUMAN_IGHV, .quant...

type:Enhancement
tag:Methods
status:In progress ⏳

Hi Dr. Nazarov, Forgive my unwiseness, I am still puzzled by some definitions, e.g. in repOverlap() fucntion, [https://immunarch.com/reference/repOverlap.html](url) **step** | Either an integer or a numeric vector.In the first case,...

type:Question
tag:Docs
status:In progress ⏳

## πŸš€ Feature Most BCR analysis programs (ex. MIXCR and IMMCANTATION) also output a field with information regarding the constant chain (ex. IGHG1, IGHA1). It would be nice to also...

type:Enhancement
tag:IO
status:In progress ⏳
tag:BCR

## πŸ“š Documentation Hi, I think it is necessary to have a doc for models of clonotype definitions, like the one in [scirpy](https://icbi-lab.github.io/scirpy/tcr-biology.html).

type:Enhancement
tag:Docs
status:In progress ⏳
tag:Single-cell

For example, if I visualize my data with vis(.by = cluster, .meta=immdata.opc.tcr$meta), the orders are determined by alphabetical. However, I would like to reorder the group into specific orders (Immune...

type:Enhancement
type:Question
tag:Methods
status:In progress ⏳