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Error with `import10xFeatureMatrix` when reading 6 files: rownames (genes) of individual RNA objects are not equivalent

9

Hi! I got the following error using 'import10xFeatureMatrix' with 6 RNA matrices, at the step of "Merging individual RNA objects": `Error in import10xFeatureMatrix(input = c("/path/filtered_feature_bc_matrix.h5", : Error - rownames (genes)...

raquel-bc

Calling peaks with MACS2 segmentation fault error

2

I've been completing the given hematopoiesis tutorial as seen here: https://www.archrproject.com/bookdown/index.html#section Is there any insight as to what may be causing these errors? **Attach your log file** [ArchR-addReproduciblePeakSet-3fd52e100b114a-Date-2022-08-10_Time-21-30-43.log](https://github.com/GreenleafLab/ArchR/files/9305645/ArchR-addReproduciblePeakSet-3fd52e100b114a-Date-2022-08-10_Time-21-30-43.log) **Describe the...

allwright1

Error in eval(parse(text = genome)): object 'BSgenome.Mmusculus.UCSC.mm10' not found

8

when I load the saved project and then use the addMotifAnnotations function, it shows this error : Error in eval(parse(text = genome)): object 'BSgenome.Mmusculus.UCSC.mm10' not found Traceback: 1. addMotifAnnotations(ArchRProj =...

yingyuan830

Monocle3 output directory not being created - Error in pdf(path, width = 6, height = 6, useDingbats = FALSE) :

5

Attempting to run the new trajectory html https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Trajectory.html Ran into following error:

sylestiel

GeneActivityScore region calculation for overlapping genes

2

ArchR's `.addGeneScoreMat` function incorrectly calculates what region flanking a gene to include in the gene score in the presence of fully overlapping genes. This issue affects about 16% of genes...

bnprks

Dev jg 0701 Show Diffs

1

jeffmgranja

save macs2 fold enrichment signal value in summits

5

Currently, the narrowPeak signal value at the summit isn't saved, and this quick fix allows this metric to be added to the replicate summits `.rds` file for downstream uses.

badoi

Originally, peak sets do not have a `name` column. This means that when `getFeatures()` is called, it returns `NULL` because no `name` column is present. This makes it impossible to...

rcorces

addArchRAnnotations() is incompatible with getPositions()

1

### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1405 Originally posted by **rojinsafavi** April 27, 2022 Not sure if this is a bug, or if I am missing something here. I added "EncodeTFBS": ```projHeme2

rcorces

Addressing https://github.com/GreenleafLab/ArchR/issues/1379 Issues with `projectBulkATAC()` when `dimsToUse` has been set.

rcorces