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Hi, sometimes when I run motif analysis,I get this error:
Loading required package: rtracklayer
Error in loadFUN(x, seqname, ranges) :
trying to load regions beyond the boundaries of non-circular…
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Hi,
I'm in the process of working my way throught the full manual of ArchR. I was wondering if generation of PseudoBulk Replicates is a prerequisite to Calling Peaks using ArchR. Also can I dire…
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Thanks a lot for developing this very useful package. I met some problems when trying to coembed the scRNA-seq and scATAC-seq data.
"pbmc.rna" is a Seurat object of scRNA-seq processed by Seurat p…
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Dear authors,
I am trying to use ArchR for 10X Multiome analysis but I meet some problems which I don't know how to solve. I guess this problem may also exist in the scATAC-seq analysis but I didn'…
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Hi Tim,
Thanks a lot for developing this very useful package. I feel confused with the integrated scATAC samples to integrate with scRNA samples. Here are my steps to integrate the scATAC and scRNA, …
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Hi Tim,
thank you for this great package.
Base on the vignettes of "scATAC-seq data integration", I have integrated the scATAC data across 2 samples. Then I have a question how to calculated the gen…
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I have human scATACseq data, so I didn't run annotateMouseToHuman and just ran directly:
se = aggregateRSEByGene(rse)
Error in assaysList[[1]] : subscript out of bounds
It seems the error occurs…
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Chris emailed with Blue Lake and came to this conclusion:
> FYI,
> Blue has clarified how Snare RNAseq & ATACseq should be classified. In short:
>
>> They both are single nucleus assays, but fo…
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I have scRNA-seq and scATAC-seq data.
Here I created a gene activity matrix and ran Harmony.
Now when I transfer the labels,
transfer.anchors
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Hi Tim,
Thank you for your reply. As your advice, I try the merge vignette, but it seems like 2 samples have a very strong batch correction.(with reference to https://github.com/timoast/signac/issue…