ArchR

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Easy bug fix for addClusters to support Leiden igraph implementation

1

**Describe the bug** Currently, the [addClusters](https://www.archrproject.com/reference/addClusters.html) parameter 'method' which can be specified as Seurat or Scran, is the same parameter name as [FindClusters](https://satijalab.org/seurat/reference/findclusters) parameter method, which is used to specify...

AmosFong1

SummarizedExperiment Error with import10xFeatureMatrix function

2

``` > ArrowFiles archr / || \\##==......\ / || ______ = =|__ /__ || \\\ ,--' ,----`-,__ ___/' --,-`-===================##========> \ ' ##_______ _____ ,--,__,=##,__ /// , __== ___,-,__,--'#' ===' `-'...

yojetsharma

Error in plotFootprints(seFoot = seFoot, ArchRProj = projHeme, normMethod = "Subtract", : unused argument (useNames = TRUE)

1

Hi, I have trouble running an plotFootprints method. **Here is code:** plotFootprints( seFoot = seFoot, ArchRProj = projHeme, normMethod = "Subtract", plotName = "Footprints-Subtract-Bias", addDOC = FALSE, useNames = TRUE,...

ttchen0714

Troubles in the tutorial with rank plots labels

1

**Attach your log file** None available. See session info below. **Describe the bug** All rank plots in the manual are plotted without the text in the labels **Example 1** The...

alekseybelikov

Troubles in the tutorial with plotEnrichHeatmap followed by ComplexHeatmap::draw

1

**Attach your log file** [ArchR-plotEnrichHeatmap-32564018f95d-Date-2024-10-25_Time-20-25-52.634833.log](https://github.com/user-attachments/files/17526717/ArchR-plotEnrichHeatmap-32564018f95d-Date-2024-10-25_Time-20-25-52.634833.log) **Describe the bug** 1) Wherever there is `plotEnrichHeatmap` function followed by `ComplexHeatmap::draw` functtion, e.g. ``` heatmapEM Error in grid.Call.graphics(C_downvppath, name$path, name$name, strict): Viewport 'Norm. Enrichment...

alekseybelikov

Error in tutorial trajectory analysis

2

**Attach your log file** [ArchR-correlateTrajectories-32567050e2a2-Date-2024-10-25_Time-19-19-59.909418.log](https://github.com/user-attachments/files/17526262/ArchR-correlateTrajectories-32567050e2a2-Date-2024-10-25_Time-19-19-59.909418.log) **Describe the bug** `trajCombined supplied assay(s) are not identical to those of the receiving > SummarizedExperiment object 'x' **To Reproduce** Reproducible in the tutorial **Expected...

alekseybelikov

AddDoubletScore - TileMatrix/chr5/rowSums does not exist

1

I am having some issues with AddDoubletScore(), I have used before on these samples however I am now getting this error message indicating there is an issue with the HDF5...

shamer3

problem in creating Arrow Files from Bam file

1

Hi I am very new to ArchR . I have downloaded a public dataset and i indexed the fastq with hg19 as they mentioned in paper.This created sam file, which...

zara03

plotMarkerHeatmap

3

When I run the code in tutorial data, I found the different heatmap whose marker genes in each cluster was not ordered？What happened? How can I draw the figure like...

l-magnificence

peakAnnoEnrichment() Error

2

Error running peakAnnoEnrichment() ``` > motifs.neg sessionInfo() R version 4.3.3 (2024-02-29) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.6.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 Random...

eblchen