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Helo! The species I studied is pig, there is no BSgenome object, how can I create it? Is ArchR only suitable for species research with BSgenome information?
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Thanks for this great package.
I am wondering if ArchR can provide a function to project matrix to low dimension,
for example, here is how Seurat does:
```
# If you wold like to observe genes t…
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[ArchR-addDeviationsMatrix-1788a61a09cea-Date-2021-01-14_Time-17-53-59.log](https://github.com/GreenleafLab/ArchR/files/5846152/ArchR-addDeviationsMatrix-1788a61a09cea-Date-2021-01-14_Time-17-53-59.…
xz333 updated
3 years ago
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Hello!
The maxDist argument in `addCoAccessibility` reads as:
"The maximum allowable distance in basepairs between two peaks to consider for co-accessibility".
In the code this distance is used …
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Hi, I was wondering is there an easy way to select the peaks only in the promoter region (+-500bp of TSS) of a certain gene? instead of showing all the peaks across all the cell-types ?
can I just ad…
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Hi, I have gone through the paper and docs these days and great work! And I have some questions in my utilization on my own data analysis when using ArchR.
1. are there any utility interfaces to e…
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I wanted to try and call peaks on the ATAC fragment file generated by CellRangerARC with MACS2 without using `CallPeaks()`, and then manually import the narrowPeaks file as a GRanges object into R usi…
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[ArchR-addGeneExpressionMatrix-27cd6ce94d9b-Date-2021-01-18_Time-22-16-01.log](https://github.com/GreenleafLab/ArchR/files/5834011/ArchR-addGeneExpressionMatrix-27cd6ce94d9b-Date-2021-01-18_Time-22-16…
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**Describe the problem that your feature request would address.**
Single-cell data sets are getting very large, even after filtering. Some might find it helpful to be able to reduce the size of these…
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Dear Archers,
I run into problems with the function addGeneIntegrationMatrix which gives the following error:
ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-13a493e8b0b4b-Date-2021-…