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What effect size value should I use for differential abundance of microbiome taxa?

effect size differetial abundance statistics written 3 days ago by deep771992chanda • 10

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1.7k

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How to calculate SNP effect size using Beta and Risk Allele Frequency?

effect size snp written 16 months ago by BobN • 10 • updated 16 months ago by zx8754 ♦ 9.7k

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A modern way to perform the analysis that LEfSe does?

microbiome effect size lefse lda written 17 months ago by ariel • 110

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6.0k

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Effect size of a SNP - contribution to genetic variance

effect size complex traits snp statistics written 3.9 years ago by Peixe • 600

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Recent Replies

C: Adapters fro nano pore sequence by krushnach80 • 840
not sure i have to ask my collaborator what exactly happened
C: How to obtain organelle genome by lieven.sterck ♦ 8.7k
if full genome is not working out for you (though a correct approach) , you could select a subset...
C: Use PCoA plot rather than phylogenetic tree? by prfsullivan • 0
Yeah, I'm a little concerned that I can't do that. One suggestion I heard to was to bin the sequ...
C: Issue installing rmats using conda by noahhelton98 • 0
I've tried both ways and get the same results.
C: Find read distribution over every gene in RNA-seq by Istvan Albert ♦♦ 85k
ah indeed `genomecov` does not do that, I meant to write `bedtools coverage` instead, for that yo...
C: How to fix this strand flips for Michigan Imputation Server? by ryshi.study • 0
Hi Guo, I also want to try this command. May I ask where do you find the reference VCF file?
C: Find read distribution over every gene in RNA-seq by Shred • 220
Ok but take for example genomecov. It gives you the output of the **whole** genome, or by each po...
A: Find read distribution over every gene in RNA-seq by Istvan Albert ♦♦ 85k
There are many tools that compute coverages over features, say `bedtools genomcov`, `featurecount...
C: bedtools questions ! can't sort/index by samtools after bedToBam command by Istvan Albert ♦♦ 85k
the command you posted does not look right, that slash in front of sample.bed indicates a file in...
C: Quantification of acetylation enriched regions at transcription factor binding s by massimofaggiani • 0
Thank you for your answer, but I managed to do that simply by adding `-c` (count) option in `bedt...
C: Information loss in .bgen to .bed conversion by MS • 20
Did you manage to sort this? See whether --hard-call-threshold helps?
C: Use PCoA plot rather than phylogenetic tree? by antonioggsousa • 1.5k
I don't think that you can do that, but I may have be wrong. So, a PCA or PCoA is a multivariat...

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