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Comment: Trouble Using GEO Files with Seurat
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I do not know if they are exactly the same, but I think they are equivalent from its description ([link](https://anndata.readthedocs.io/en/…
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You are welcome. I have to be completely honest and say that I do not have experience with other modalities rather than scRNA-seq. Though c…
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https://www.biostars.org/p/357878/
Mind the details and effort part.
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A. may be the most correct, but I think you are making some incorrect assumptions about READ1 and READ2, so that I don't think any of these…
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To maybe add more context, Drug at 0h and Placebo at 0h should be equivalent samples, since they are effectively both "untreated".
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I have not compared results as you suggest, but logically, there is a functional difference. Whether this has a great effect depends on the…
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stop using venn diagram. Use Upset plot instead. There are some upset plots in journals at https://plottie.art/search?q=upset&loaded_pages=…
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> Use of fastp: Even if no adapters are detected, would you still recommend using fastp for consistency across datasets?
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7 is the max I've seen, though even [6 sets usually starts to look pretty stupid](https://www.nature.com/articles/nature11241/figures/4). I…
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Both the drug and placebo must be brought to the common frame of reference (0h) before they can be compared to each other. If you did `Drug…
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Hi, we just added bedMethyl support! Try it at https://genome-test.gi.ucsc.edu/cgi-bin/hgTables. type must be "bedMethyl". Please let us kn…
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BED files have specific format. https://genome.ucsc.edu/FAQ/FAQformat.html#format1
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