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Lasso regression and cross-validation on RNA seq dataset
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Is it possible to run haplotypecaller in gnu parallel ?
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Recent Replies
Comment: R: problem with running time-series analysis software: Mfuzz
by
Kevin Blighe
81k
Cross-posted: https://support.bioconductor.org/p/9144396/
Answer: Lasso regression and cross-validation on RNA seq dataset
by
Mensur Dlakic
★ 18k
It is not clear whether you have 192 datasets or 192 features in some undefined number of datasets, but either way cross validation is a sm…
Comment: SARS-CoV-2 lineages complete reference genomes
by
GenoMax
115k
I don't know if the following two resources are going to provide `reference` genomes. You may have to go to GSAID for that.
Answer: SARS-CoV-2 lineages complete reference genomes
by
GenoMax
115k
From EBI: https://www.covid19dataportal.org/sequences?crossReferencesOption=all ![EBI][1] [1]: /media/images/04dd9b11-77a8-4327-8…
Answer: Software to draw protein domains of proteins
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cmdcolin
★ 2.1k
tools mentioned by other users are great, a couple more tools here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag…
Answer: SARS-CoV-2 lineages complete reference genomes
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GenoMax
115k
At [**NCBI SARS-CoV-2**][1] resource page. Be sure to switch to `Nucleotide` tab and then click on pango lineage search. ![Pango][2] …
Answer: comparisons between 2 ChIP-seq datasets
by
jared.andrews07
★ 13k
Honestly, I'd just eyeball the tracks in IGV. It's usually pretty apparent. If you want more objective measures, you could look at total…
Comment: data correaltion
by
Jeremy
▴ 130
FYI the cor.test() function will display a p-value in addition to the correlation coefficient.
Comment: Inflation in Imputed data
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desicasares@gmail.com
▴ 10
Thank you for your answer...the populations I am using are Spanish, North European and Italian individuals. In the case of the Italians t…
Comment: MAF in R
by
malgorzata.sobczak07
• 0
You're the best! Thanks! :)
Comment: Help with kallisto-bustools: how to interpret the inspect.json output file
by
dsull
★ 3.0k
Correct, which is why you should load your output into R or python and filter your cells (i.e. do the "knee plot"). See the kallisto | bust…
Answer: MAF in R
by
Ram
36k
You can use `HardyWeinberg::maf` to calculate MAF from a vector of frequencies. You can create this vector of HOM/HET/HOM-ALT frequencies u…
Comment: MAF in R
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malgorzata.sobczak07
• 0
Yeah, sorry :)
Comment: MAF in R
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Ram
36k
Your code won't work. You'll need to quote the allele strings
Comment: The minor allele frequency
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Negatyvna
• 0
Yes, I would like to do the second option
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