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Recent Replies
Answer: Best strategy for comparing cell-type composition between disease and healthy gr
by
jared.andrews07
★
19k
I'd recommend reading the [differential abundance testing chapter](https://bioconductor.org/books/3.21/OSCA.multisample/differential-abunda…
Comment: How do you clean GEO metadata before downstream analysis?
by
yura.grabovska
▴
800
They did make a [Tool post originally](https://www.biostars.org/p/9613596), but still phrased it as something they just came across rather …
Comment: How do you clean GEO metadata before downstream analysis?
by
jared.andrews07
★
19k
Agreed, just make a "Tool" post if you want to spread the word about it.
People tend to take those much better than these weak attempts at…
Comment: RNA-seq assigned alignments
by
GenoMax
152k
Since you have decided to move to a new sequence provider that decision is for economic reasons and not scientific, so not much to think ab…
Comment: Obtain Common SNPS for Mouse Genome
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GenoMax
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These are multi-strain VCF's so you could look for SNP's common across the strains (see --> https://www.biostars.org/p/9498113/ ) . Keep in…
Comment: RNA-seq assigned alignments
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Manko47
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>Are you comparing the same exact library sequenced by two different companies.
Nah it's just majorty of my old datasets osciliated around…
Answer: RNA-seq assigned alignments
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GenoMax
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> Previously on the single-end data from old company I was getting around 50-60% of the uniquely aligned reads
Are you comparing the same…
Comment: Extract track data from "search by region" feature on ENCODE
by
AlienPumpkinPie
•
0
Thank you for your reply! Yeah I thought the same. It feels weird to me that this is not an obvious feature.
Comment: How do you clean GEO metadata before downstream analysis?
by
yura.grabovska
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800
Again... "I recently *stumbled* upon a small browser-based tool"
On the site: "Created by alba0gf"
That's the second time you've linked y…
Comment: Tool to clean GEO metadata
by
yura.grabovska
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"i recently *found* this simple tool"
Go to site
"Created by alba0gf"
I mean... why lie?
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yura.grabovska
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What do you think you'll gain by doing tumour vs normal at single-cell resolution? The whole point of single cell is to define sub-populati…
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ZuelTech
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My purpose is to count reads mapping to the genomes. Was my code above in doing so correct?
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Mensur Dlakic
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Maybe this will work, minus the flux data.
https://www.kegg.jp/kegg/pathway.html
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Unless you are able to use "user defined window" with color (as noted in https://art-egorov.github.io/lovis4u/ExampleDrivenGuide/cmd_guide/…
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What is your analysis goal? Differential methylation? edgeR has a workflow (see its user guide) where 6 vs 1 would be supported. That is ob…
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