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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,
I'm trying to used PEAS on my own ATACseq data. I have already extract all the feature and performed a model using chromHMM.
My issue is that, the chromHMM output is a .txt file and it's s…
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RNA_seq
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Hello, I want to report that when I'm running my analysis, I'm getting the following error:
Error in dimnames(x) warnings()
Warning messages:
1: The dot-dot notation (`..count..`) was deprecated…
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@stemangiola and I can provide materials and advice
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From: Anne Carpenter
Date: Fri, Dec 1, 2023 at 2:44 PM
Hi Ardigen/Ksilink,
Using this attached plot from Ardigen of the top 25 most anti-correlated pairs, I saw MYT1-RNF41.
So, I found someon…
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I have just started exploring use of DMRcate for DMR detection but have concerns about the approaches dmrcate offers for ranking DMRs. DMRcate offers Fisher's combination, Stouffer's combination, and …
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Hi,
I have been trying to run your pipeline on the mm10 data set (as setup by running install_genome_data.sh ). As there were no fast files, I made a bam file from the bed files and am running the…
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Hi,
The instructions of how to run CreateNetwork are truly murky because there is no folder called "annotated_tfbs" nor is there an example file. After a lot of head-scraching this is what I hav…
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When simulations break right after a new generation initialized, they leave behind a `out/[simOutDir]/[variant]/[seed]/generation_######/` directory which contains a `000000/simOut/shell.log` output t…