Questions tagged [epigenetics]

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limma linear model with interaction

I want to run some epigenome wide association studies based on city and pollutant type, could you please suggest if I can get DNA methylation sites (CpG) association based on pollutant type for each ...
bioinfonext's user avatar
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Statistical approach to link DNA methylation with toxic element exposure and health outcome

I would be thankful to you if you can help with the statistical approach for case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
bioinfonext's user avatar
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Mendelian randomization

I would be thankful to you if you can help with how I can use MR from my case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
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DNA methylation mediator analysis for environmental exposure and health outcome

We measured blood DNA methylation using epic array in 100 no-diabetic and 100 type 1 diatbetic patients matched for age, sex and smoking and also measured arsenic exposure using ICP-MS. Could you ...
bioinfonext's user avatar
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Enrichment analysis of DMPs | new Ilumina EPIC V2 900K

Im analyzing methylation data from the new illumina's EPIC V2 array (900K). I would like to perform enrichment analysis on DMPs. In the past, I have always used missMethyl but since there are a lot of ...
Julieta's user avatar
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obtaining a fragment data file bed from bam

Im trying to follow this pipeline https://github.com/epifluidlab/cragr on cfDNA WGS. I have bam files from paired end reads aligned with bwa mem. The workflow requires bgzipped and indexed fragment ...
Julieta's user avatar
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1 vote
1 answer
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Association analysis for methylation beta value and phenotypes in R

I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with ...
bioinfonext's user avatar
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How to determine a correct promoter sequence? (Bisulfite sequencing)

I'd like to ask you for help with an university assignment. First let me post the entire question: Design primers for bisulfite sequencing of the promoter of the ACE2 gene in microbat Myotis ...
Matěj Nemec's user avatar
2 votes
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WGBS vs ONT, which one should I trust?

First of all let me apologize if this is not the place for this question. While it can be quite broad, I will try to make it as specific as I can. Context I am testing the correlation between Whole ...
Paul Endymion's user avatar