ArchR

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Problem How to convert archr project into seurat

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Hi, @rcorces @jeffmgranja @jgranja24 @keyuxi I would llke to copy my entire ARCHR project cluster, embedding, umap ... into a seurat object but I do not succed to copy embeddings...

A-legac45

can't install ArchR on my mac Sonoma 14.6.1

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devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories()) If your issue persists, then please submit this bug report. PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE....

yeroslaviz

Error when using addClusters() on multiome data

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Hello, Thank you so much for creating such a great tool. I really appreciate how thorough you are in the manual and do a great job of explaining what you're...

klgoss

Why hasn't ArchR been updated?

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Currently, many new analytical needs have emerged in single-cell ATAC-seq. Why doesn't ArchR consider accommodating them?

superSXB

Not All Seqnames Identical!

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Hi all, I am having an issue with addIterativeLSI , using TileMatrix , I get this error: ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-34f754ef9709-Date-2024-08-12_Time-22-18-58.603256.log If there is an issue, please report to...

Aya-Balbaa-72

SOLUTION: addGeneExpressionMatrix / import10xFeatureMatrix issue

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I just wanted to add some information about the addGeneExpressionMatrix and import10xFeatureMatrix functions in case anyone else is running into the same issue I had. The error message I kept...

juliabelk

getValidBarcodes() need to be modified to compatible with the output of Cell Ranger ATAC version higher than 2.0

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**Describe the bug** Hi there, I‘m using ArchR to analysis my ATAC data. And I want to do barcode filtering in `createArrowFiles` step. I found that `getValidBarcodes` could help me...

cherrie-g

subset archr project

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hi, i was try to subset the archr project according the cell type, the bigger archr project has call peak and when i subset and when i try to call...

XiaoKaixuan12333

Extrating out the getMarkerFeatures

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I have two samples in my ArchR file. I need to compare them. So I used the getMarkerFeatures to do a pairwise comparison in my data. This gives me Log2Fold...

mano2991

addMonocleTrajectory is throwing an error - Error in .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj")) : could not find function ".validInput"

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**Attach your log file** I am unable to get a log file for this call. **Describe the bug** THis used to work before but now it says could not find...

susrinivasan