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Hi all!
I have a problem with the LSI function, I get the following error. I want to analyze single cell( Atac-seq) data for two mouse samples.
I figure out that running an each sample separately …
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ArchR's `.addGeneScoreMat` function incorrectly calculates what region flanking a gene to include in the gene score in the presence of fully overlapping genes.
This issue affects about 16% of gene…
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Is there an easy way to directly generate a `plotPeak2GeneHeatmap` by plotting the filtered Peak2GeneLinks after using `addPeak2GeneLinks` ?
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```
> ArrowFiles archr / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--'…
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Hi, I am using the plotMarkerHeatmap in ArchR and my code is
- plotMarkerHeatmap(
seMarker = markersPeaks,
cutOff = "FDR = 3",
labelMarkers =NULL,
transpose = F,
pal = viridis(n=256…
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### Discussed in https://github.com/GreenleafLab/ArchR/discussions/2141
Originally posted by **icenzano** March 28, 2024
Hello everyone! I am starting with multi-omics analysis and I need to a…
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I am using the `addClusters` function with `method = "Seurat"` and `resolution = 0.8`. While clustering 9 samples takes approximately 9 hours, clustering 35 samples has already taken over 180 hours. I…
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Thank you very much for developing this tool. However, I encountered a problem while actually running the addReproduciblePeakSet process."
neuron_1
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Hey. I have the same error showing up. Please note that i have run ArchR on the same dataset previously and it had worked. Here is the error and the sessioninfo along with output of the logfile. I get…
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Hi @rcorces, I tried using this approcah but ended up with this error:
devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories())
proj