ArchR

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cannot create custom genome for mm39 using TxDb and BSgenome

1

**Attach your log file** ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag...

sidwekhande

ERROR createArrowFiles : core dumped

1

I am performing analysis on a non-model species, and I encounter a "core dumped" when creating an arrowfile. I'm not sure what could be causing this, and I haven't found...

minghao622

Seurat FindClusters() Error when running addDoubletScores() and addIterativeLSI() ----> no slot of name "i" for this object of class "Graph"

6

I am getting this error when running addDoubletScores() as well as addIterativeLSI() `no slot of name "i" for this object of class "Graph" ` And it seems to originate in...

solvi808

Error not all FeatureDF for asssay is the same!

1

getTrajectory(ArchRProj = proj, name = "tj1",useMatrix = "PeakMatrix", log2Norm = TRUE,smoothWindow = 30,groupEvery =1) Error in .getFeatureDF(getArrowFiles(ArchRProj), useMatrix) : Error not all FeatureDF for asssay is the same! Hi！ I...

schnappi-wkl

How to deal with dsciATAC data, it's about 50,000 cells per sample.

1

I'm working with an object which is about 50,000 cells per sample. When I use ArchR addDoubletScores() function to inferring dsciATAC-seq Doublets, there are only a few cells can be...

Goood2001

Error creating ArrowFiles : Character(0)

2

When running ArchR with default parameters (threads set to 1) and inputting the ArrowFiles command into the terminal to ascertain whether any ArrowFiles have been created I receive an error:...

SaharBJ

Error when subsetArchRProject

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Hello, **Attach your log file** This step doesn't generate a log file. **Describe the bug** I tried to subset a ArchR project with the code below: proj2=subsetArchRProject( ArchRProj = proj1,...

fe4960

test pull request for comparing changes

rcorces

predictionCutoff parameter in addPeak2GeneLinks

1

### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1814 Originally posted by **RegnerM2015** January 19, 2023 Hi @rcorces and @jeffmgranja , I was looking at the source code for `addPeak2GeneLinks` and the use of predictionCutoff:...

rcorces

P2G error with addPermutedPval

19

Hi @rcorces, I tried using this approcah but ended up with this error: devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories()) proj

AnjaliC4