immunarch

immunarch copied to clipboard

repOverlap on complete nucleotide sequence?

1

Hi, apologies if this is a rather simple issue, however, I was wondering if it would be possible to modify the overlap() function to calculate overlap based on the Sequence...

dl-mallory

repLoad question for MiXCR

7

Hi, I am working with immunarch to analyse my paired RNA data, and I am facing a technical issue. I used MiXCR to get full TCR/IG sequence using "assembleContigs" parameter....

parkjaeming

Problems with Repload for 10x data

2

Hi I am starting to use Immunarch for 10x sc paired data. Thanks for implementing it! I have loaded a dataset where my samples are defined by the Column "Cluster"....

annecar

Support for File Formats of Bcellmagic/Immcantation Toolset

7

Hi, I would like to use Immunarch for my bulk TCR-seq data which was analyzed with the bcell magic pipeline: https://github.com/nf-core/bcellmagic When loading my data with repload, it doesn't load...

nkric

Hope the document can show the multisamples input workflow in 10X cellranger VDJ

2

Hi, Thanks to develop the great tools for immunolgical analysis of multiple data format. with the development of VDJ repertoires, it would be a milestone in years to come. In...

honghh2018

Question regarding the scdata dataset

4

Hi! Thank you so much for this very useful tool! I have a question regarding the scdata object provided as an example dataset. It contains bc_patient and bc_cluster where each...

samcwj

CDR3 length with paired(?) data

1

Hi, thanks for making this tool! I am trying to read in cellranger data from 10x following [](https://immunarch.com/articles/web_only/load_10x.html) and to do some data exploration. ``` immdata % vis() ``` ...

npklein

Support for bulk TCR deconvolution (TRUST4)

2

Hi, I would really like to use some of the functionality in immunarch. I have TCR sequences from bulk RNA-sequencing data that I inferred with TRUST4 (https://github.com/liulab-dfci/TRUST4). According to the...

Michael-Geuenich

Clonotypes across timepoints - why does it merge more than one clone?

3

Hi, When I use this command: tc2

venchi9

Where can I find the barcode for single cell identify from the returned object of repLoad ?

1

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....

zh-zhang1984