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Hi all,
I had a question regarding what is best if you have more than the max number of replicates. For example, one of the conditions in my experiment has 14 biological replicates. My initial though…
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Biosamples with ATAC only data are missing commas separating the tissue and sex/age
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Currently, there is no submission code for scAtac.
Since we no longer use DNANexus for submission, it makes to develop a new API for scAtac or snRNA
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Dear authors
I recently came across the publication "Epigenetic regulation during cancer transitions across 11 tumor types" and was impressed by the massive scale analysis you have performed.
I…
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Hi there,
I calculated the gene activity scores for my dataset and realized there was a bias toward more abundant populations. Is there any way of performing this calculation on the averaged acces…
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Multiome ATAC Library remove index selection from Multiome ATAC Library.
Remove Total column from Pre-Amp Reagents
Look for dead onChange/onRender functions
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Thank you for adding the input datasets for the tutorials.
I’m currently going through the “Mouse Pancreatic Endocrinogenesis (scATAC-seq) | Training with an RNA-Dynamics kNN-Graph” tutorial and e…
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Hi!
I am using SCENIC+ and I am having an issue in the 'Generate pseudobulk ATAC-seq profiles, call peaks and generate a consensus peak set' step.
I am using the following code to create the bed…
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Hi, thank you for this great package! I encounted a bug "ValueError: invalid literal for int() with base 10: 'X'" when my peak list contains peaks from "chrX" and "chrY". Those peaks are neglectable, …
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Hi there,
Thanks so much for creating this package. I'm in the processing for trying it for one of my samples.
I have bulk WGS and 10x scATACseq (also paired scRNAseq; outputs generated by cellrange…