ArchR

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Add CCA batch correction method

1

Addressing https://github.com/GreenleafLab/ArchR/discussions/1695 Implementing a CCA-based batch correction method within ArchR (for example as used by FindIntegrationAnchors -> IntegrateData within Seurat/Signac).

jblich870

in order to pass the `R CMD INSTALL` step

waddella

on newer R versions these dependencies on base packages need to be stated explicitly in order to pass `R CMD INSTALL`

waddella

error when subsetArchRProject

1

I can run subsetArchRProject successfully for every sample, but when I run for one sample, something wrong happend! Command is: archR_object = subsetArchRProject(ArchRProj = archR_object, outputDirectory = archr_out, cells =...

EddieLv

when running addGeneIntegrationMatrix function, it will occur this error: "Error in slot(object = object, name = \"features\")[[layer]]

ZhangFuchang

installing ArchR on conda

2

Hey! I've been having serious problems installing ArchR on Conda. I've added the YAML file and shown the outputs of a failed installation. I've tried running this on multiple versions...

Mashazhefer

Configuration failed, installtion of dev branch on no-network-machine

1

Hello, I tried to install dev branch ArchR on a network-restricted machine (only specific sites allowd to access, such as github, CRAN, etc.) and got errors as below: ``` *...

ZeroLi-Bio

PeakCallTiles-groupMat: Error in vapply(all_objects, nrow, integer(1L), USE.NAMES = FALSE) :

1

[ArchR-addReproduciblePeakSet-47655b744492-Date-2024-06-11_Time-11-14-47.log](https://github.com/user-attachments/files/15785993/ArchR-addReproduciblePeakSet-47655b744492-Date-2024-06-11_Time-11-14-47.log) ``` Error in vapply(all_objects, nrow, integer(1L), USE.NAMES = FALSE) : values must be length 1, but FUN(X[[2]]) result is length 0 Calls: addReproduciblePeakSet ... Reduce -> f -> rbind...

drowsygoat

Error in g$grobs[[legend]]: no such index at level 2, when calling peaks

5

I encountered this error during call peaking, while the call peaking process has been completed. However, I got an error message that says "Error in g$grobs[[legend]]: no such index at...

nansne

cannot open connection

1

Hi i am getting this error for the same code and same versions of packages i used earlier where i did not got any errors. [archr error.docx](https://github.com/user-attachments/files/15744035/archr.error.docx) [archr error.docx](https://github.com/user-attachments/files/15744029/archr.error.docx) Can...

chsnys