ArchR

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Can not install ArchR by downloading zip from github under conda environment

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To install ArchR, I created a conda environment and installed R4.3.2 as well as related packages. Since the server I use can not connect Internet, I can only download zip...

Qiuyanhe

A spelling error in Manual.

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jiangpuxuan

Error when running addIterativeLSI

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Hello, cellchat is a wonderful tool！ I ran into the same issue with running addIterativeLSI with my data. code： scATAC

QianhuiXu

addIterativeLSI error

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When I run the addIterativeLSI with my data the error message was appeared. 2023-09-18 10:32:02 : Computing Estimated LSI (projectAll = FALSE), 0.358 mins elapsed. ************************************************************ 2023-09-18 10:32:24 : ERROR...

khsjh

ArchRProject

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**Code** > ArrowFiles > 'arrows''D19-13000.arrow''D19-8612.arrow''D19-8613.arrow' > brain1 ...... test all three of them, all three of them can be created successfully. However: with all the ArrowFiles, it shows error: >...

TingTingShao

Error addGeneIntegrationMatrix "Error in .getPartialMatrix(getArrowFiles(subProj)"

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Hi @rcorces I tried to integration scRNA and scATAC, but I get the following error: - seuratRNA_2 An object of class Seurat 31053 features across 7264 samples within 1 assay...

ZayaAyush

Add rworkflows GitHub Actions

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Hi @rcorces , now that it's reached maturity I thought you might be interested in using `rworkflows` for running continuous integration directly in GitHub Actions. You can read more about...

bschilder

Error during addDoubletScores

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Hi! I was running the tutorial code on tutorial data but couldn't get past doublet scoring. I keep seeing this error. Could you help have a look? Thanks! ``` >...

yangshichen0713

Quick fix for output directories requiring no spaces. I understand it is not the best practice to have spaces in path names. However, I don't believe this should be a...

arprieve

addGeneIntegrationMatrix fails with tutorial dataset and Seurat 5.0.0

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**Attach your log file** [ArchR-addGeneIntegrationMatrix-12d1d6685d430-Date-2023-11-11_Time-17-32-30.524157.log](https://github.com/GreenleafLab/ArchR/files/13326109/ArchR-addGeneIntegrationMatrix-12d1d6685d430-Date-2023-11-11_Time-17-32-30.524157.log) **Describe the bug** In the [ArchR tutorial section 8.1](https://www.archrproject.com/bookdown/cross-platform-linkage-of-scatac-seq-cells-with-scrna-seq-cells.html) running `addGeneIntegrationMatrix` fails, with the error: ``` Error in slot(object = object, name = "features")[[layer]]

chloeacolson