ArchR

ArchR copied to clipboard

Different group labels for the same predicted cell in integrated scRNA

4

Hi, I have noticed strange behavior when adding GeneIntegrationMatrix. I have posted a Discussion several months ago but I think it might be useful to open an Issue as well....

Zepeng-Mu

.testMarkerSC() failing when mean1 and/or mean2 is NA during call to getMarkerFeatures()

3

### Discussed in https://github.com/GreenleafLab/ArchR/discussions/1319 Originally posted by **wuv21** March 3, 2022 Hi! Been running into an issue similar to #562 and #483 with the same error output, but I have...

rcorces

Error in arrow file creation (.addGeneScoreMat): "HDF5. Dataset. Unable to initialize object"

6

Hi, I have an issue that I suspect may be related to the recently fixed error (https://github.com/GreenleafLab/ArchR/issues/395) in saving tile matrices when there is no coverage (short scaffold). During arrow...

dagarfield

Issue with addPeakAnnotations for Custom Deviations

7

**Attach your log file** [ArchR-addDeviationsMatrix-c27565ce590-Date-2021-09-16_Time-12-11-10.log](https://github.com/GreenleafLab/ArchR/files/7179433/ArchR-addDeviationsMatrix-c27565ce590-Date-2021-09-16_Time-12-11-10.log) **Describe the bug** I am trying to create a custom deviation (following chapter 13.2.3), but while the addPeakAnnotations step completes, the resulting matrix is unavailable....

agalianese

Bug in addBgdPeaks() function

3

Hi, I'm trying to compute motif deviation. I did peak calling, and everything went well. Unfortunatly, I get the following error when I try to add background peaks to my...

CSBioAzim

1. I could not get projectBulkATAC to work without as.array(.getAssay(subATAC, "counts")) 2. I am probably the only relatively sensible person who uses spaces in folder names (as I am forced...

scfurl

Mitochondrial genes removed at import10xFeatureMatrix

5

Hi Jeffrey and Ryan, I was testing the multiome pipeline following the tutorial below. https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html However, I found out that at the import10xFeatureMatrix function, all the mitochondrial genes were removed....

kosekijkk

Issue in .getFragsFromArrow (and thus addGroupCoverages) when nFrags = 1

3

I ran into a small issue when running addGroupCoverages on my terrible non-model species genome. [ArchR-addGroupCoverages-765f62f12d5f-Date-2021-04-18_Time-23-35-59.log](https://github.com/GreenleafLab/ArchR/files/6332245/ArchR-addGroupCoverages-765f62f12d5f-Date-2021-04-18_Time-23-35-59.log) > addGroupCoverages(ArchRProj = projSpurp_doubletRemoved_filtered2, groupBy = "Clusters_doubletRemoved_filtered", threads = 1, force = TRUE) #just...

dagarfield

Full Manual PDF - Page not found 404

1

Hello, The full manual PDF is showing up a page not found error (https://www.archrproject.com/bookdown/ArchR.pdf). Could you please fix this? Thanks, Kaivalya

Kaivalyamolugu

The provider_version slot was replaced with the genome argument of metadata slot in the new version of BSgenome.

0CBH0