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HI Fang,
I am analyzing two different cell lines, each cell line have the wild type and Knock out subtypes. All the 4 samples are sent to 10x scATACseq at the same time. I walked through all your …
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Dear developers,
I found that there needs a PWM format text as input in the config file. However, Jaspar only provides PFM text and the R library construct a PWMatrixlist how to get the PWM format …
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Hello,
I was trying to use ALTRE to perform some differential accessibility analysis on my mouse ATAC-seq data and ran into problems while following the vignette. Although I have loaded and read in m…
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Hi @matthiaskoenig,
Could you please let me know if we can view the differential equations in the report that is generated via SBML4HUMANS?
I could view the fluxes in the report but not the differ…
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Hi, Ricard @rargelaguet
I am reproducing Extended Data Fig. 6a of the article "Multi-omics profiling of mouse gastrulation at single-cell resolution" . I have currently downloaded Supplementary Table…
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Hi,
As I am becoming more familiar with NucleoATAC, I am realizing you do not have a way to set a normalization factor, how would you suggest doing that? I used S2 nuclei in my ATAC-Seq to be abl…
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We are thankful that you are producing this document, which we believe has genuine potential to shape better outcomes for AI and the web.
One aspect which you don’t address is the need for public p…
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On the call on October 26, 2023 the problem was brought up about what an implementation should display when there is a conflict between the ONIX and Schema.org accessibility metadata present inside t…
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hi @joschif, congrats on the publication and thank you for porting the analysis in a package!
I would like to ask for an advice for analyzing a 10x multiome dataset (control and condition with mult…
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Hi, first thanks for the package, it seems to work nicely. I however have a couple of questions that I think can be clarified in the Docs or somewhere else:
1. When peaks do not have equal width, a w…