scDblFinder

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Error in installing scDblFinder: object ‘colBlockApply’ is not exported by 'namespace:beachmat'

3

Hi, I installed scDblFinder by `BiocManager::install("scDblFinder")`. When I ran `library(scDblFinder)`, I got this error message: ``` Error: package or namespace load failed for ‘scDblFinder’: object ‘colBlockApply’ is not exported by...

amber4mint

How to find all features used in training

1

Hi scDblFinder team! It's mentioned in the paper that scDblFinder utilizes multiple features obtained from the Knn network, such as projections on principal components; library size; the number of detected...

XinyeZhao

SCTransform example in vignette not working

1

**Describe the bug** I'm trying to replicate the example in the vignette to use SCT internally within scdblFinder but I get the error below > Error in if (length(sel_features) >...

JesseRop

Removing genes from count matrix before doublet detection

3

Hi, I want to remove some rRNA contamination-related genes from my scRNA count matrix. Should I use scdblfinder after or before removing those genes? I know that cell filtering isn't...

kiwipeel

Unable to run scDblFinder - "as_cholmod_sparse" does not exist

5

I'm working on a Seurat object that has been normalised and scaled and I now want to find the doublets. ``` sceobj

sunnlife1978

scDblFinder error when using aggregateFeatures and knownDoublets

2

Dear developers, I'm working with multiplexed (CMO) scATAC-seq data (one 10X-run has 6 samples) which gives me information on known doublets from overlap of hashtags. When using the `scDblFinder` function...

dottercp

Where to run scDblFinder in SCT workflow

1

Hi, I wanted to double-check where I should run scDblFinder in my workflow (Seurat v5). For context, I have 4 conditions, with 3, 3, 2 and 2 samples each (total...

shaln

Wild Variability in doublet scores

2

Hi, thank you for the excellent tool. I was looking at the variability in scores between different runs on the same data and was very surprised to see barcodes called...

markddesimone

dbr.per1K and equivalent dbr gave different number of doublets removed

5

Hi, I am running scDblFinder using dbr.per1K (0.004) as well as manually calculated dbr (ncol(sre)/1000 * 0.004), they two should be equivalent from my understanding, however they resulted in different...

MengjunWu

Different results between using merged object or object separated by samples

1

Hi, Thank you for developing the tool. I'm working on a dataset that has >200 samples. I want to test out the codes so I tried on one sample first,...

AdelynTsai