mihem
mihem
Dear immunarch team, thank you for the user-friendly and highly useful package. After loading 10x VDJ data `filtered_contig_annotations.csv` via `repLoad`, I run into problems when running `repGermline` which is required...
**Describe the bug** When opening a Rmd template, lintr does not work and shows the following error: ``` failed to run diagnostics: ! in callr subprocess. caused by error: !...
Using `IntegrateLayers` without specifying `group.by` is slow. With my ~ 400 000 cells dataset, only the "preprocessing" before the actual integration, takes rather long (~10 min). If I specify `group.by`...
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I would like to map cells, simiar to this tutorial https://satijalab.org/seurat/articles/covid_sctmapping, but with the `RunAzimuth` wrappers. ``` sc_small_hlca str(sc_small$RNA@layers, max.level = 1) List of 2 $ data :Formal class 'RenameDims'...
A minor bug/inconsistency in the azimuth pbmc labels is that CD56bright NK cells are called `NK_CD56bright` in `seu_object$predicted.celltype.l2` but `NK-CD56bright` in the feature names. I like to create FeaturePlots of...
Issue initially reported here: https://github.com/satijalab/seurat/issues/7879 Integration preprocessing took long (~10min in my case with 120 000 cells and 61 layers). Time was nearly completely spent on ```Seurat:::CreateIntegrationGroup``` , more specifically...
Added bindings for `R create terminal` in `R` and Quarto` mode. This is relevant because `Run Selection` does not automatically start an R Terminal when `r.alwaysUseActiveTerminal` is set to true....
@ncborcherding Hi Nick, sorry, not sure this is within the scope of scRepertoire, but in my current project I would like to annotate iNKT (and maybe MAIT). This is possible...
@joseah `SeuratObject` is listed in NAMESPACE, but is missing in DESCRIPTION. This goes as far as failed installation of `SeuratWrappers`, which has `Nebulosa` as a remote dependencies, which should misses...