ArchR

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addGeneExpressionMatrix incorrectly calculates "Gex_MitoRatio"

1

This is a quick fix but users should know that when doing any kind of multiome analysis, `addGeneExpressionMatrix()` is not accurately calculating `Gex_MitoRatio`. There are two sources of error here...

dannyconrad

Unconstrained integration error - "more elements supplied than there are to replace"

1

Hi I am running unconstrained integration and getting the following error, which seems to stem from the slots/layers ArchR is pulling from the seRNA (Seurat object) input. `2024-03-14 12:11:53.67366 :...

LacquerHed

GGplot Errors for Fragment Size Distribution and DoubletScores

3

I am getting errors with anything related to ggplot. I have done as suggested in previous thread by reinstalling Cairo, Quartz and ggrastr, however this has not fixed the problem....

shamer3

Error in plotTrajectoryHeatmap that set labelMarkers failed

1

When use the function plotTrajectoryHeatmap(), I set the parameter labelMarkers, but it'sis not working.

xiaochanmin

Error in subsetArchRProject

1

Hi, I encountered an error when I tried to subset project by sample names, here is the code: dd=split(proj2@cellColData,proj2$Libname) for (i in names(dd)){ subsetArchRProject( ArchRProj = proj2, cells = getCellNames(proj2[proj2$Libname==i,]),...

jinbufan

Is scaleDims scaling along the wrong axis?

4

I read the issue threads #323 & #447 because I've been working a lot with the LSI components of my datasets lately. I think I found the source of the...

dannyconrad

ERROR Found in .fastTSSCounts for creating arrowfile

1

Hi, I have trouble creating an arrowfile. I have non-standard chromosomes for our fragment files, so I customized the geneAnnotation and genomeAnnotation which have the same seqnames with our fragment...

macrophage666

Sparse_Marginsum Error Running IterativeLSI

9

Hello, I'm trying to subset a cell population in mouse samples from my existing ArchR project and re-run clustering/dimensional analysis. I'm able to subset and create a new project but...

S-Rajhans

[error] addDoubletScores function: "addIterativeLSI" - tutorial data

4

**Describe the bug** Hi. According to the log file, I keep getting an error which is found in `addIterativeLSI` for one of Arrow files generated using the tutorial dataset when...

jinhys

error of addGeneIntegrationMatrix : <simpleError in dimnames(x) <- dn: length of 'dimnames' [1] not equal to array extent>

5

[ArchR-addGeneIntegrationMatrix-171f8742a45cc6-Date-2023-12-01_Time-16-51-22.log](https://github.com/GreenleafLab/ArchR/files/13523077/ArchR-addGeneIntegrationMatrix-171f8742a45cc6-Date-2023-12-01_Time-16-51-22.log) This is an issue template made by the developers of ArchR. You MUST follow these instructions. HI, when i use addGeneIntegrationMatrix , i meet the question of

XiaoKaixuan12333