Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: Cutadapt installation - user defined directory
... [Bash Environment Modules][1], although Python virtual environments are extremely useful, so I'd consider your choices carefully. [1]: http://modules.sourceforge.net ...
written 1 day ago by andrew.j.skelton735.1k
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Comment: C: why Dseq2 does not care about the condition?
... You could keep everything as is, and just specify the contrast you're interested in. Check out `?results` > results1 <- results(dds, contrast=c("condition","Tumor","Normal")) > results2 <- results(dds, contrast=c("condition","Normal","Tumor")) ...
written 18 days ago by andrew.j.skelton735.1k • updated 17 days ago by Ram16k
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Answer: A: why Dseq2 does not care about the condition?
... condition <- factor(c(rep("Normal", 10),rep("Tumor", 11))) condition2 <- factor(c(rep("Tumor", 11),rep("Normal", 10))) levels(condition) [1] "Normal" "Tumor" levels(condition2) [1] "Normal" "Tumor" The levels of your factor variable are the same (alphabetical unless ...
written 18 days ago by andrew.j.skelton735.1k
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Comment: C: Best Digital Marketing Agency in Delhi
... Hello savimehtaa! We believe that this post does not fit the main topic of this site. Spam For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be happy t ...
written 23 days ago by andrew.j.skelton735.1k
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Answer: A: Installing MultiQC on Ubuntu
... pip install multiqc --user ~/.local/bin/multiqc ./my_qc_reports_dir/ ...
written 25 days ago by andrew.j.skelton735.1k
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Comment: C: Create a File format to store Variant
... Well, you can certainly have a multi-sample annotated VCF file, however you're correct in that sample wise meta data is typically captured by pedigree files. ...
written 25 days ago by andrew.j.skelton735.1k
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Answer: C: Create a File format to store Variant
... ![enter image description here][1] The VCF spec is capable of capturing extra metadata around variants, including gene information, see tools such as VEP or annovar. Granted it's not the most glamorous of implementations, but it works. To do this you'd have to have a tool that converts from VCF to ...
written 25 days ago by andrew.j.skelton735.1k
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Answer: A: Programming interview via Skype
... When I've done / issued these kinds of tests before in interview, it's usually on a shared notepad - ie you'll be given a link to follow and you can write pseudocode / in the language of your choice - The interview panel will typically be able to see as you type. A lot of the time what I'm trying to ...
written 4 weeks ago by andrew.j.skelton735.1k
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Comment: C: RNA BULK SEG ANALYSIS
... The term you're looking for is differential expression. There's lots of tools out there, but generally [Limma Voom][1], or [DESeq2][2] are the packages of choice. In future, members of the community will be a lot more receptive if you've shown some effort in trying to answer the question yourself. T ...
written 4 weeks ago by andrew.j.skelton735.1k
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Comment: C: edger model matrix design of linear model
... You're right, the data frame initialisation was wrong. I mostly wrote this as pseudocode and ran bits in R...I probably should have written that as a disclaimer. Setting the seed has benefits in reproducibility, but as it's proof of concept, and dummy data, it doesn't really matter here. ...
written 5 weeks ago by andrew.j.skelton735.1k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Surrogate Variable Analysis for Complex Experimental Design
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