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Can't run mixcr 4 with the external reference

7

Hi, I was running mixcr 3 with the IMGT reference like so: ``` mixcr analyze amplicon --species mmu --starting-material rna --5-end no-v-primers --3-end c-primers --adapters no-adapters --library imgt --threads 8...

Original identities not respected in ATAC analysis

1

I noticed that unlike RNA analysis, the original identities aren't assigned to the Seurat object when using `ATACRunSeurat`. I propose to add the same behaviour where: - The `orig.ident` is...

FeaturePlot not setting correct axis limits with custom reduction

2

I've added custom dimensionality reduction to my Seurat object, as well as pseudotime values. The DimPlot look alright: FeaturePlot is way off: In this case, I have to set the...

Highlight single cluster

3

Thanks for the package, it made my analyses much more enjoyable! I'm wondering if there's an easy way to highlight just one cluster with `plot_hexbin_feature_plus`. I guess there's no support...

COVID19 Bronchoalveolar lavage fluid scRNA-seq

Hi, Thanks for sharing! What kind of hardware did you use for running this?

As a heads-up, I don't think the following works with the latest `Seurat`: ``` epi.seur = SetIdent(epi.seur, [email protected]$phenograph.k750) fib.seur = SetIdent(fib.seur, [email protected]$phenograph.k250) imm.seur = SetIdent(imm.seur, [email protected]$phenograph.k250) ``` I updated the...

getContentUrl is deprecated.

1

Branch.getContentUrl() is deprecated. Is there any updated example?

Running on M1 macs

6

This is a long shot, but I'll try anyway. I'm trying to run this with Docker on M1 Mac. Here's the error: ``` ➜ nextflow nextflow run nextflow-io/rnaseq-nf -with-docker N...