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I used the following command to create a Snakefile following the instructions at https://github.com/liulab-dfci/MAESTRO/blob/master/example/RNA_infrastructure_10x/RNA_infrastructure_10x.md.
Unfortu…
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@jgranja24 @rcorces, I would like to have access to the meta cells data matrices both for scRNA-seq and scATAC that are used to link peak to the gene in **addPeak2GeneLinks**
Is it possible to output…
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Hi there.
When working with my own scATAC-seq data derived from pre FACS-sorted cells I was never able to identify mitochondrial variants which achieve the thresholds (log10(VMR) > -2 & strand > 0.65…
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Hi Tim,
I am using FindMarkers to identify significant differential accessible peaks from scATAC-seq data. We are using min.pct = 0.05 and logfc.threshold = 0.25 as cut-offs. However, this analysis…
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Hi,
Is it practical to run Find Variable Features when analysing scATAC seq data in Signac.
Do we still use vst for that purpose. What is the recommended nfeatures for the same?
Thanks,
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Running the official ArchR [tutorial](https://www.archrproject.com/bookdown/creating-arrow-files.html) with the example data keeps getting stuck at createArrowFiles at "Batch Execution w/ safelapply!"…
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Hi all, thank you for an amazing, easy to use and well-documented package that allows relative bioinformatics newbies to start doing quite sophisticated analyses.
We are a GWAS lab and would be int…
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Hi,
Thanks a lot for developing this very useful package. I met some problems when trying to coembed the scRNA-seq and scATAC-seq data. My code is listed as below:
"pbmc.rna" is a Seurat object…
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[ArchR-addPeakAnnotations-165f957dadfc2-Date-2020-12-28_Time-02-49-15.log](https://github.com/GreenleafLab/ArchR/files/5747014/ArchR-addPeakAnnotations-165f957dadfc2-Date-2020-12-28_Time-02-49-15.log)…
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https://mp.weixin.qq.com/s/i9Vj01rzEPmCMtqNsg27dg
ixxmu updated
3 years ago