ArchR

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GroupCoverage file path doesn't update saveArchRProject

6

Hello and thanks for the great tool, I would like to re-open the [closed bug issue #529](https://github.com/GreenleafLab/ArchR/issues/529) - I am also getting the same problem that my GroupCoverage file path...

evaham1

addGeneIntegrationMatrix reductions parameter

1

Hello, **Describe the bug** [A clear and concise description of what the bug is.] If you set a reduction parameter others than the default "cca" options, the code will not...

Goultard59

Unable to run getMarkerFeatures()

1

Hi! I have been using ArchR for awhile now but recently ran into issue with using getMarkerFeatures function: Error in .logThis(cellNames, "cellNames supplied", logFile = logFile) : object 'logFile' not...

vincycheng

Will the arrow files being subset running subsetArchRProject() with dropCells = TRUE?

1

Hi ArchR developers, I was trying to subset the archr project for a few samples after QC using subsetArchRProject() and setting dropCells = TRUE. These samples were successfully removed from...

qdong2023

Error in h5read(x, paste0(useMatrix, "/Info/Units")) : Object 'GeneExpressionMatrix/Info/Units' does not exist in this HDF5 file

1

@rcorces I encountered the issue with GeneExpressionMatrix. After installing the ArchR from devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories()), I can successfully import the RNA h5 files and add the gene expression...

qdong2023

Merging or Combining multiple ArchRProject Objects

1

Hello ArchR developers, I have several ArchRProject objects that require merging. These ArchR objects originate from distinct batches of arrow files and experiments from 10x multiome kits. It's important to...

qdong2023

How to conduct footprint analysis for loci of a single gene across different celltypes

1

Current analysis pipelines only include celltypewise footprinting analysis. However, if the object is to investigate how a single gene is regulated during some import biological process, there's no accessible codes...

OMIC-coding

Error in addGeneIntegrationMatrix / abnormally high number of communities

12

When executing the code provided, the following error occurs: ``` > mRCCv5 An object of class Seurat 22921 features across 102723 samples within 1 assay Active assay: RNA (22921 features,...

Khreat0205

Error in plotEnrichHeatmap:

1

Problem: After running the code: enrichMotifs

erlun1

mapLabels function

1

I want to subset a cluster from archr project by running clustree. on this specific cluster and put it back to the archproject. ##### subset cluster9 idxSample

A-legac45