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I am working on ATAC-seq mice data and have developed a function to run bias model training across all folds and comparison groups. While testing the function with fold 1 and the group fed_vs_fasted_0…
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Hello,
I was wondering if TEpeaks would work for ATAC-seq peaks? Have you ever tried it?
Thank you
Rita
RRebo updated
5 months ago
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T cell subsets are likely best distinguished w/ ATAC-seq data so we should track down some.
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I think it would be good to include the results of this benchmarking paper in the ATAC-seq processing section. It does a quantitative comparison of various libraries in the ecosystem and compares them…
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Cell by bin
Visualize in higlass
Cell by peaks (in BED + snap files)
Annotated peaks (genomic intervals) per cell
Genome-wide (not necessarily tied to a gene)
Our Pipelines:
- [ ] We need to cre…
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Hi,
thanks for this great resource!
It's especially nice that you provide the peaks here given that the raw data is under restricted access and it's quite a pain to get it (I've been waiting for a m…
plger updated
2 weeks ago
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I have non-single cell ATAC-seq data, can I use SnapATAC2 to analyse it?
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Hi!
I was following the tutorial for integrating scRNA-seq data and scATAC-seq data using the dataset provided. However, I get the following error when I run the step: atac = tfl.findNeighbors(adat…
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Hello,
I've got a question. I would like to try your software to perform peak calling, but instead of using Chip-seq data I woul like to use it on ATAC-seq data.
Do you think it is possible? If so,…
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Hi @smorabit,
I would like to know if it is possible to use hdwgcna with single Cell ATAC coverage data instead of the SC RNA-seq expression matrix. How should the metacells function be handled? Wh…