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Is it possible to have a workaround to import data using only the 10X feature matrix alone (`matrix.mtx.gz`, `features.txt.gz` & `barcodes.txt.gz`) as many public data in GEO is in this format.
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Hello,
Thank you for creating this tool, it is extremely useful. And, congratulations on your recent publication.
I keep getting this error when I try to add gene expression from a multi-omics proj…
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Hi @rcorces and @jgranja24 and @AliciaSchep
**Where is the problematic documentation?**
Section 13.1 (ChromVAR)
**Describe what is unclear or confusing**
Is it possible for ChromVar to accoun…
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[ArchR-addGeneExpressionMatrix-b89d48e52328-Date-2021-02-11_Time-16-14-52.log](https://github.com/GreenleafLab/ArchR/files/5968735/ArchR-addGeneExpressionMatrix-b89d48e52328-Date-2021-02-11_Time-16-…
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I used the cisbp database to do motif enrichment analysis. And I checked the PWMatrix and converted it to PPM matrix with the following command:
PWMatrixToProbMatrix
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PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE.
**Attach your log file**
[ArchR-plotEnrichHeatmap-7fc6549babd-Date-2020-12-17_Time-11-59-13.log](htt…
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https://mp.weixin.qq.com/s/CVXsJPPx12saw0WYiReQag
ixxmu updated
2 years ago
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Hi @jgranja24 and @rcorces ,
Would you be able to elaborate on the alternate peak calling method in section 10.3 of the User Manual?
Does it simply find enriched tiles or do individual tiles get…
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> https://github.com/GreenleafLab/chromVAR/issues/82
> https://github.com/r3fang/SnapATAC/issues/211
I also run this error, How Can I slove this problem....thanks
when I was run ChromVAR Devi…
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In the ArchR publication **ArchR Methods – Marker Peak Identification with Annotation Enrichment** part, it says
> Additionally, when selecting these bias-matched cells ArchR will match the distri…