ArchR

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No rownames for peakmatrix from the ArchR project

1

I have the ArchR project load into `proj` ``` getAvailableMatrices(proj) [1] "GeneScoreMatrix" "PeakMatrix" "TileMatrix" ``` To get the peak matrix I used: `peak_matrix peak_matrix class: RangedSummarizedExperiment dim: 187739 15031 metadata(0):...

venkan

Harmony package installed and loaded but when attempting addHarmony, the package 'does not exist'

1

[ArchR-addClusters-2b6f85f90f9-Date-2023-08-08_Time-12-25-49.log](https://github.com/GreenleafLab/ArchR/files/13279417/ArchR-addClusters-2b6f85f90f9-Date-2023-08-08_Time-12-25-49.log) When using the addHarmony function: proj1_Oct2

SaharBJ

plotMarkerHeatmap cannot produce the plot

2

Hi, I am using the plotMarkerHeatmap in ArchR and my code is - plotMarkerHeatmap( seMarker = markersPeaks, cutOff = "FDR = 3", labelMarkers =NULL, transpose = F, pal = viridis(n=256),...

travilucas

Hi, I just modified the code for plotting the trajectory heatmap and made it being able to plot for positive TFs. No other algorithms are added. I wonder is there...

Sky970415

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

2

I used my own peakset, but failed, plz help me, I beg u. proj2

Alpha-LiCan

Error Report - addGeneIntegrationMatrix()-Attempting to add a different number of cells and/or features

1

Hi, I also occurred similar problem. The seRNA is a seurat object. The column name of seRNA@assays$RNA@counts is different from archrproject$Cellnames. I modifies the name by following code: ``` seRNA_2

yetingliytl

Another error with addIterativeLSI - "Error in clusterDF$clusters : $ operator is invalid for atomic vectors"

2

This seems to be a new bug because I did not get this before, I am suspecting it might have something to do with the new Seurat version as Seurat...

solvi808

Error in addDoubletScores

3

Hi! When I use the tutorial data to run the sample code, I keep encountering this error. I also try to set threads=1, but it still appear same error. I...

zhangyina

createArrowFiles has encountered an error

1

Can't create arrow files for own data but the function works fine with tutorial data [ArchR Log File.zip](https://github.com/GreenleafLab/ArchR/files/12602606/ArchR.Log.File.zip) [ArchR-createArrows-15669c21d8f02f-Date-2023-09-13_Time-10-38-21.log](https://github.com/GreenleafLab/ArchR/files/12602761/ArchR-createArrows-15669c21d8f02f-Date-2023-09-13_Time-10-38-21.log)

gmcregis

addReproduciblePeakSet could not get same result

1

I call peaks by celltype, but I get different result use same database. And the seed in R had set.

zhangqc723