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Hey!
Can you share your code for generating bed file that contains 500 kb windows for each gene
Thank you!
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**Attach your log file**
ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it her…
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I've tried this on two different MBPs (macOS 10.14 and 10.11), with two different R versions (4.0.4 and 3.6.3), both with fresh installs of ArchR v1.0.1. I can't use v1.0.0 for my pipeline because add…
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Hi Authors,
I am trying to run SCARlink on some of our own data. I was able to run and finish the tutorial successfully.
All packages are installed as per the instructions.
To elaborate - We ha…
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Hello :-),
I am trying to use your function "plotClusters".
However I am getting the error: "Error in xtfrm.data.frame(x) : cannot xtfrm data frames" when I try to run it.
I have used DeSeq2 to…
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Hi everyone, I am using ArchR to integrate scATAC-seq data with scRNA-seq(using addGeneIntegrationMatrix function), and I got these errors below. I have tried many possible solutions but failed, inclu…
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Hi Jeffrey and Ryan,
Thank you so much for developing this wonderful tool and we are actively using it for 10X scATAC-seq and multiome analysis. I'm following https://greenleaflab.github.io/ArchR_2…
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I have created custom genome with your guides.
![image](https://user-images.githubusercontent.com/54537420/84038015-eeed2780-a9d1-11ea-922b-c3412295f73e.png)
![image](https://user-images.githubuserc…
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**Describe the bug**
when i run getMatrixFromProject(proj,useMatrix = "GeneScoreMatrix").The error message is as follows:
ArchR logging to : ArchRLogs/ArchR-getMatrixFromProject-44db558acd0bf-Date…
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When I use creatArrowFiles function I meet the warning The index file is older than the data file :fragment.tsv.gz.tbi.I would like to ask what is the reason for this and can i ignore this?The referen…