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Is there no mitochondrial chromosome or mitochondrial gene annotation in [chm13v2.0.fa.gz](https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz) and […
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Dear dpcook,
just a tiny "issue" - you used the human regexp "MT-" for detecting mitochondrial genes. Use "mt-" instead and your plot showing mitochondrial gene distribution will no longer be flat.…
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Dear Velocyto.R developer,
I have a technique question and would like to ask you. I checked mitochondrial genes in the loom file using Velocyto.R and noticed that they all have 0 expression (code b…
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I hope this message finds you well. I am currently encountering some difficulties while running a program, and I would greatly appreciate your assistance in resolving these issues.
> library(SingCe…
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Hi! I really appreciate for developing this powerful tool.
I met a puzzling event - there were no any MT-gene detected in some of my scTE csv files, which could be found in starsolo matrix.
Why did…
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Hi developer,
Thank you for creating such a fast and helpful software; it's been very useful for my work.
My objective is to remove rRNA reads and retain only those reads that do not contain rRNA…
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This cluster was found in #7 as strong (+/-) correlation in both ORF and CRISPR but not (completely) strongly connected in the KG.
Looking across ORF and CRISPR plots there, there are a few other …
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I do encounter the following error after importing 10X spatial h5 object when performing the RunICA function:
`Error in validObject(.Object) :
invalid class “DimReduc” object: rownames must be …
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Hi,
For NucSeq data I would expect that mitochodrial genes are to a large extend caused by ambient RNA and in previous versions they have been removed well for most samples. However, in v0.3 this i…
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Hi @evanpeikon
Thank you for sharing this analysis. Interestingly, I get similar numbers of cells and genes, but I don't transpose the AnnData object. I end up with nearly identical numbers of gen…