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2 votes

WGBS vs ONT, which one should I trust?

Methylation can be cell-specific, which makes it difficult to evaluate accuracy on a bulk-cell level (even within the same tissue). How can you tell that the differences you're seeing are due to ...
gringer's user avatar
  • 14.3k
2 votes

obtaining a fragment data file bed from bam

There's an example in the README (https://github.com/epifluidlab/cragr#example-datasets): For you information, below are steps from the BAM file to the fragment file: ...
jared_mamrot's user avatar
1 vote

Statistical approach to link DNA methylation with toxic element exposure and health outcome

Having given some thought to this, I'd still use machine learning. I would attempt to augment the negative controls however. Is there a suitable published data set? R program is caret but it high ...
M__'s user avatar
  • 12.6k
1 vote

Mendelian randomization

I understand linkage disequilibrium (LD) versus panmixia, which the technical term for Mendelian randomisation and for humans PLINK is a population package. The best outcome is a correlation between ...
M__'s user avatar
  • 12.6k
1 vote

Enrichment analysis of DMPs | new Ilumina EPIC V2 900K

We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vignette: https://www.bioconductor.org/packages/release/bioc/...
Daisy Fu's user avatar
1 vote

WGBS vs ONT, which one should I trust?

I would assess directionality and accuracy of prediction by 1) WGBS predicting ONT and then 2) ONT predicting WGBS. Firstly, I would use deep learning (or machine learning) and train WGBS against ONT, ...
M__'s user avatar
  • 12.6k

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