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**Describe the problem that your feature request would address.**
I am working with a dataset that has multiple technical replicates for every biological replicate. As a result, a collaborator gave …
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Hello,
I've been trying some of the multiome functionality in ArchR, I've generally had good results, but have run into an issue with addPeak2GeneLinks(). In issue #361 it is suggested that this fu…
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**Attach your log file**
[ArchR-addReproduciblePeakSet-7d5d6a3f1cf2-Date-2021-04-07_Time-22-26-07.log](https://github.com/GreenleafLab/ArchR/files/6272434/ArchR-addReproduciblePeakSet-7d5d6a3f1cf2-Da…
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Is generating DotPlots supported?
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[ArchR-addArchRAnnotations-c8613ddc2be3-Date-2021-01-27_Time-13-01-57.log](https://github.com/GreenleafLab/ArchR/files/5882447/ArchR-addArchRAnnotations-c8613ddc2be3-Date-2021-01-27_Time-13-01-57.lo…
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Hi,
I have been trying to using with features addGeneIntegrationMatrix with features specified (forwarded to Seurat::TransferData). Unfortunately this runs into an error. I believe the features arg…
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Hello,
I have a dataset in which there is a common progenitor that gives rise to 4 different differentiated cell types (i.e. cluster 1 to cluster 2, cluster 1 to cluster 3, etc.), so there is only…
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Adding genome from `BSgenome` object produces the error similar to #393
To reproduce it:
```
library(ArchR)
library(BSgenome.Dmelanogaster.UCSC.dm6)
genomeAnnotation Getting genome..
> Getting …
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Hi,
I do cluster my scATAC-seq data, and for downstream analysis, I want to only select specific cell type (let's say cell type A), and do subclassing and continue the rest of analysis with this sub…
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Hello,
I have both scCITEseq and scATACseq data. I know how to add scRNAseq data to my ArchR project but I wandering to know if there is a way to put the information regarding the surface cell prote…