ArchR

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Can't install the ArchR on MacOS 15.0.1

7

**Describe the bug** I followed suggestions from previous posts to revert to an older R version (e.g. 4.1.3) because ArchR would not install with the updated R 4.4. However, I...

penghy27

Peak marker heatmap not sorted

1

PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. **Attach your log file** [ArchR-plotMarkerHeatmap-1819e726ff2fd-Date-2024-10-22_Time-13-56-44.070744.log](https://github.com/user-attachments/files/17476660/ArchR-plotMarkerHeatmap-1819e726ff2fd-Date-2024-10-22_Time-13-56-44.070744.log) **Describe the bug** Peak marker heatmap is not sorted unlike...

alekseybelikov

Error in g$grobs[[legend]]: no such index at level 2

3

When run the tutorial "https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html" The output figures are all correct but when I tried to save them: ```{r} #Save Plot plotPDF(p1, p2, p3, name = "UMAP-scATAC-scRNA-Combined", addDOC = FALSE)...

danli349

`addGeneIntegrationMatrix` Error in slot(object = object, name = "features")[[layer]] <- features: more elements supplied than there are to replace Traceback:

5

When run the tutorial in the document: https://www.archrproject.com/bookdown/cross-platform-linkage-of-scatac-seq-cells-with-scrna-seq-cells.html ```{r} projHeme2

danli349

`addGeneExpressionMatrix` Error: invalid subscript

1

Hello How can I `addGeneExpressionMatrix` using a `SingleCellAssay` object? I created the `SingleCellAssay` object by: ```{r} seRNA

danli349

Problem with addMonocleTrajectory( ArchRProj = NULL, name = "Trajectory", useGroups = NULL, groupBy = "Clusters", monocleCDS = NULL, force = FALSE )

1

Hello, I am trying to use this fonction but NA are return in the trajectory_monocle column I chek and cell names are identic between archr and cdsmonocle I do not...

A-legac45

plotMarkerHeatmap: nLabel = 0 will result in an error

1

I don't want to show the task marker (peak information) on the side when drawing. Please help me. The code and error are as follows： >heatmapPeaks

huyulan-funan

`createArrowFiles` can't generate "QualityControl" plots

2

I run the codes in the documents: https://www.archrproject.com/bookdown/per-cell-quality-control.html ```{r} ArrowFiles

danli349

Suggestion in .createGroupBW

1

Dear ArchR developers, While trying to integrate the createGroupBW in Signac I realized that I think there is a small mistake in: https://github.com/GreenleafLab/ArchR/blame/d9e741c980c7c64e5348c97a74d146cc95f8ba76/R/GroupExport.R#L340 I think it should be: ``` i...

lldelisle

simpleError in validObject(.Object): invalid class “DimReduc” object: dimensions for ‘cell.embeddings’ must be in order

3

When run the tutorial "https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html" ```{r} #Add Clusters proj

danli349