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Hi
First thank you for developing this amazing tool.
I am using scenicplus in a ubuntu server conda environment, which is not a root account.
i was in a peak calling stage but an error which …
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Can I use output from cellranger-arc in cellbender ?
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Nice tool, congratulations! I would like to use it on 10x ATAC/multiome data. Could you please explain the following?
1. It would be great to see an example of how to start from `fragment.tsv.gz` s…
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In cell hashing or CITE-seq datasets, an additional count matrix is produced and it stores how many ADT/HTO barcodes (see this for details https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13…
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Hi! I am trying to use SnapATAC2 for my analysis. It would be a really package for my needs so thanks for developing it!
I tried to install using ```pip install snapatac2``` --> success as far as I…
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Hi, I am trying to run `addGeneIntegrationMatrix` with a Seurat object, and am running into an error. My guess was that the `groupRNA` parameter should be `orig.ident`, as is common with most Seurat …
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Hi,
I was running the [Integrating scRNA-seq and scATAC-seq data demo](https://satijalab.org/seurat/articles/atacseq_integration_vignette.html) with Seurat v3, and the program quits with a segmen…
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Hello, thanks for muon!
I was trying to reproduce the steps described in the ATAC tutorial (https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/pbmc10k/2-Chromatin-Accessibility-Pr…
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Hi,
Great package for analysing scATAC-seq. I was wondering, is there is a way to export the per cluster coverage as wiggle tracks or bigwig file ? While the CoveragePlot function does the job, thi…
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Hello,
I am following the tutorial to preprocess snRNA-seq and snATAC-seq data. The steps below have not finished after 16 hours.
scglue.data.lsi(atac, n_components=100, n_iter=15)
sc.pp.neighb…