ArchR

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tutorial data run createArrowFiles error

1

[ArchR-createArrows-12d75115a5294-Date-2023-09-04_Time-18-21-59.353936.log](https://github.com/GreenleafLab/ArchR/files/12512805/ArchR-createArrows-12d75115a5294-Date-2023-09-04_Time-18-21-59.353936.log)

felixlee0608

error in addGroupCoverages(ArchRProj = mp, groupBy = "Sample")

2

Hello, I found an error in this mp mp traceback() 6: stop(errorMsg) 5: .safelapply(seq_along(availableChr), function(x) { .logMessage(sprintf("Kmer Bias %s (%s of %s)", availableChr[x], x, length(availableChr)), logFile = logFile) message(availableChr[x], "...

yangchao4

`subscript out of bonds` error when adding motif annotations

1

Hello, Thanks for this great software suite. It's been working great for me so far, except I keep running into the following error when I try to add motif annotations....

ndejay

Bug in addGeneExpressionMatrix using Mouse Data

3

I tried the most updated 1.0.3 and Developer version. When using the addGeneExpressionMatrix MitoRatio and RiboRatio are not calculated when using mouse data. It seems the issue is within the...

Nahuck

idxATAC not match

1

Hi, I am using the getPeak2GeneLinks in ArchR and my code is `p2g=getPeak2GeneLinks(Archproj,corCutOff=0.2,resolution=1,returnLoops=F)` and I got the following results:  I know that the results of idxATAC are stored in...

xmliu01

error addGeneIntegrationMatrix: formal argument "groupRNA" matched by multiple actual arguments

8

This is an issue template made by the developers of ArchR. You MUST follow these instructions. Questions related to how to use ArchR or requests for new features should be...

tingxie2020

How to investigate specific gene target using ArchR?

1

So far, all the vignettes have been focused on cluster-scale analysis, but all can we use ArchR to investigate the regulation mechanism for one gene. For instance, I want to...

OMIC-coding

How to transform Signac (Seurat) object into ArchR ?

1

Dear developers: After your answer, I have found a new Seurat object contains all the related ATAC information. Is it possiable to transform the Seurat object into ArchR object? Thank...

wanglu2014

Error with addReproduciblePeakSet() in finding MACS2

3

Hi, thanks for the great package. I am tweaking some data I have and need to remake an ArchR projects with new peak set. I ran the addReproduciblePeakSet() command below...

cristanchoa

Error in subsetArchRProject: Error in loadArchRProject(path = outputDirectory) : all(file.exists(zfiles)) is not TRUE

6

I noticed that when I used the subsetArchRProject function, there was a problem about `file.exists`. The following is the detailed related content: **Describe the bug/Browse code information** ```R > idxSample...

YuZhengM