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I have to process a scATAC-seq dataset with over 48,000 cells after merging three conditions and 2 replicates each condition. I kept 200,000 top peaks. The scATAC_cellranger_count.py can finish succes…
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Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development (https://www.nature.com/articles/s41467-022-28067-4)
The scRNA-se…
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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…
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Hi,
Thank you for your great tools for single cell multi-omics analysis. I successfully ran the cite-seq demo but failed to ran our scRNA+scATAC data with following error report:
The input …
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Hi,
I have a question of using scGPT on ATAC data. The typical scATAC-seq has binarized values 0 and 1, so how to make the ATAC counts as bins? Should we only make the counts to only 2 bins: 0-bin an…
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Chromap is indeed an ultrafast tool. Thanks for developing and this method.
However, I have encountered two problems when I using chromap with scATAC-seq data.
The first one is that when I analyze…
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Thanks you for developing snapATAC tools,
and i have a question:
I followed the "Integrative Analysis of PBMC scATAC-seq and scRNA-seq" pipeline.
1. drawing the prediction score in histogram…
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Hello. Thank you for this package. I'm doing an integration analysis using more than 40 scATAC samples. However, I do not have scRNA data from the same cells. I tried doing the label transfer using th…
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Hi
I was curious to know if the C.Origami model can be used on single-cell ATACseq data?
regards
Arch
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When I ran the tutorial of [Regulatory network analysis through intergrating scRNA-seq data and scATAC-seq data](https://jiang-junyao.github.io/IReNA/scATAC+scRNA), I can't found the file named P1_CM_…