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I've been using `ProjecTILs` and the CD4/CD8 human T cell reference atlases in some scRNA-seq work lately and it has been very useful for us. I wonder whether you or @ncborcherding (via https://github…
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Usually, for a scATAC-seq data, I have 1M peaks, and I wonder How many peaks should we select when using midas?
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Hi, I have some unpaired scRNA-seq and scATAC-seq data, they are sequencing the same samples, but in separate scRNA-seq and scATAC-seq assays, so the cell barcodes are different in these datasets. How…
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Hi there,
Thanks for providing such an interesting tool for the research community.
I am testing the pipeline on scATAC-seq tumor samples only. How to work around "Step2. Unbiased segmentation ba…
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Can this platform be used for shallow scATAC-seq data? I have output from cellranger atac count pipeline. How can I generate doubletD inputs from this?
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I went through both the vignettes that are available. However, I was wondering if there was more on how to generate the .rds files for scRNA (sparsematrix) and scATAC seq (SummarizedExperiment).
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Hi,
I am trying to download the [scATAC-seq data](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178324) and remap it to hg38. I just wanted to double check that I got the experimental design …
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Very useful and easy to use tool!
I wanted to ask if DoubletDecon can be repurposed for scATAC-seq doublet detection. Theoretically, you could run DoubletDecon on the **gene activity matrix** crea…
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Dear epiAneufinder team,
Thank you for your excellent work and for providing the community with this wonderful package. I have run epiAneufinder on our scATAC-seq dataset comprising 20 donors from …
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I am following the Wiki to run: (see the screenshot attached)
All my bam and tsv files are generated correctly but when I am trying run the .sh file attached, I encountered a .slurm file and it…