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Ran a project with reference peaks, but I am unable to generate a count table for the reference peaks:
When the project is run:
1) peaks are still called for each sample individually
2) Each sample…
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Hello,
I would like to go through the tutorial, but the link (www.readthedocs.io/mubind) for single-cell genomics data in the data availability section of the paper does not seem to work.
Could…
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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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https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
This is the single bad option. If fixed-up, tutorial's entire wf runs great at ORG :)
…
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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…
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**Use case**
My data consist of BAM paired-end files already filtered by duplicates, mit reads, etc. (99% alingment)
**Describe the problem**
I tried to use this command in bash
macs3 hmmratac…
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- [x] Remove "(beta)" from title of track hub
- [x] Change "general cCREs" to "Cell-type Agnostic cCREs" and this should always appear as the first "folder" of the track hub display
- [ ] For select…
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I have non-single cell ATAC-seq data, can I use SnapATAC2 to analyse it?
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editor preferred term: single-nuclei ATAC-seq
alternate terms: snATAC-seq
textual definition: Analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples th…