ArchR

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Sudden Error in DoubletScoring; worked perfectly fine previously

3

I have been using ArchR for a while now and had got quite far in terms of analysing my data. I have recently started trying to analyse a new dataset...

shamer3

The subset of markersPeaks cannot be processed for peakAnnoEnrichment.

1

After I subset markerspeaks, I enriched motif. Why are there subordinate errors? When I use the overall markerspeaks, I can do it normally. ``` markersPeaks

HaixJiang

Long Computation Time for addClusters with Multiple Samples

3

Long Computation Time for addClusters with Multiple Samples Dear ArchR Development Team, I am currently using the ArchR package for analyzing my single-cell ATAC-seq data. I have encountered an issue...

limiao20

speed up addClusters

1

I am using the `addClusters` function with `method = "Seurat"` and `resolution = 0.8`. While clustering 9 samples takes approximately 9 hours, clustering 35 samples has already taken over 180...

limiao20

How can I fix an error in the creation of Arrow Files from my fragment files?

3

# ArchR log file [ArchR-createArrows-73c43a8d3823-Date-2024-05-20_Time-18-57-29.805596.log](https://github.com/GreenleafLab/ArchR/files/15422822/ArchR-createArrows-73c43a8d3823-Date-2024-05-20_Time-18-57-29.805596.log) # Description of the bug While creating Arrow Files from a fragment_file_name.tsv.gz, I get an error ggplot for Fragment Size Distribution. The message says the...

Axbxh

Arrows are being created, but then unknown error, and arrows are deleted. No trace of the error in the log file.

1

I already installed dev version of ArchR (1.0.3), downgraded to R 4.1, and switched off sub-threading. For tutorial files with hg19 genome the workflow works correctly. However, for my data...

drowsygoat

Error in (function (..., threads = 1, preschedule = FALSE) : Error Found Iteration 1 :

2

Thank you very much for developing this tool. However, I encountered a problem while actually running the addReproduciblePeakSet process." neuron_1

wenhai-cell87

I noticed that the current package has introduced `version` argument, along with other new arguments in the `addMatToArrow` function, https://github.com/GreenleafLab/ArchR/blob/65968a4068253783fe6b0918efcbf7d216a49ee7/R/ArrowWrite.R#L105-L126 but the higher-level function `addGeneExpressionMatrix` does not support passing those...

szcf-weiya

Creating ARROW files :ERROR Found in .fastTSSCounts for (Mock1 : 1 of 1)

2

My log file: [ArchR-createArrows-2a3c284c353742-Date-2024-04-15_Time-01-37-40.623548.log](https://github.com/GreenleafLab/ArchR/files/14999684/ArchR-createArrows-2a3c284c353742-Date-2024-04-15_Time-01-37-40.623548.log) **I removed chromosomes that are reported to be detected 0 Fragments** according to the log file by adding `excludeChr = chromosome_ids` when creating ARROW file. I...

YaoyJiang

ERROR Found in .addGeneScoreMat TmpGS for PBMC

2

**Describe the bug** Here's a bug I encountered creating ArrowFiles, the following is my code : ``` library(ArchR) addArchRGenome("hg38") if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") library(BSgenome.Hsapiens.UCSC.hg38) genomeAnnotation

zcaiwei