SingleR

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Parallel computing fails on HPC cluster

1

I am running SingleR something like below on a unix HPC cluster. ``` library(celldex) library(scater) library(SingleR) library(BiocParallel) bp bploop.lapply In addition: Warning message: In parallel::mccollect(wait = FALSE, timeout = 1)...

royfrancis

SingleR and FindAllMarkers with Seurat Object using SCTransform v2

1

Hi Christoph, I appreciate all your work. I have a question related to SingleR and Seurat objects. I integrated two datasets using CCA-based method after scTransform normalization. The discussion in...

Chris-lang478

Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'

1

Hello, When running the following code: ``` pred

msteph11

SingleR issue

3

Hey Guys! I have been stuck on this issue for the past couple of days. I am not too sure where I could have gone wrong. I followed alll the...

sivaraja23

Errors in creating pred.hesc

1

Hello, when I was executing the following scripts: pred.hesc

rustylakeparadox

Not all clusters were annotated when "per-cluster" method was used

1

Thanks for developing this wonderful tool for scRNASeq! I've been using "per-cell" method to annotate my data, it worked very well. Recently, I started to use "per-cluster" method to annotate...

Evenlyeven

Can I use logFC values from a scRNA-seq data for trainSingleR?

1

Hello! I have a table of gene name, pval, avg_logFC, and labels (output from Seurat FindConservedMarkers) and I was wondering if I can use this for trainSingleR? Thank you so...

mkim0327

Modifications of DatabaseImmuneCellExpressionData() for epithelial cells?

1

Hi, I'm attempting to use some code that was written for single cell sequencing by someone else, however, I realized that it was written only for immune cells, not epithelial...

jasonmli

Error in .setup_groups

1

I transformed an integrated and clustered Seurat object into SingleCellExperiment. When running SingleR: _Error in .setup_groups(groups, x, restrict = restrict, exclude = exclude) : need at least two unique levels...

bigzero61

plotScoreHeatmap color parameter

8

Hi there, I would like to use my own colour scheme for SingleRs heatmap. I think there may be a bug in the plotScoreHeatmap method. When I execute the following...

alanaleah89