immunarch

immunarch copied to clipboard

pubRep gives allele instead of gene

1

Hi Team. Hope you are well. I was wondering if you can help me with something please. When I run the following command on the practice immdata dataframe; pr.aav

Alexander230

## ❓ Questions and Help I'm a new user of immunarch and was wondering if I could get a couple clarifications regarding the documentation! These are specific to the raref...

HyprValent

https://immunarch.com/reference/select_clusters.html I found this site, but I cannot split. Currently, cellranger can merge clonotype csv files into one csv file, and we can add meta data columns like "donor", "Patient"....

amufaamo

Cellranger Data Loading

1

While loading the cellranger data (10X), this is the error I encounter. -- [4/14] Parsing "/jsimonlab/users/bshim/Shuntaro_scRNA_TCR/Pool142_Cellranger/Pool142_Pt1_R/outs/all_contig.bam.bai" -- Warning: line 1 appears to contain an embedded nulError in stri_trim_both(string) : invalid...

bshim181

``` r library(immunarch) #> Loading required package: ggplot2 #> Loading required package: dplyr #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag...

royfrancis

.data is a vector.

chunxuan-hs

Depends are discouraged for data.table: https://github.com/Rdatatable/data.table/issues/3076 (in fact, we hope that R will eventually deprecate this mode of dependency) I used {lintr} to find all {data.table} usages in your package....

MichaelChirico

Hello, Any plot I make where I need to compare samples by group, the groups are always listed alphabetically. Is it a way to position them in specified order? Example...

makarov-ccf

My code: #load the package into the R environment: library(immunarch) library(dplyr) file_path = "yard/run_cellranger_vdj/run_vdj_S5/outs/aim" immdata_10x % seqCluster(seqDist(bcr_data), .fixed_threshold = 3) bcr_data %>% repGermline(.threads = 1) bcr_data %>% repAlignLineage(.min_lineage_sequences = 2)...

liu9756

Hi I have seen this thread and have the same issue. https://github.com/immunomind/immunarch/issues/174 In October 2023 there's a fix implemented in next version of immunarch. I am wondering if there's a...

paulrbuckley-kcl