Bioconductor ReadBismark

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BiSeq readBismark

updated 9.4 years ago by James W. MacDonald 68k • written 9.4 years ago by Neel Aluru ▴ 460

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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30

I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…

Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k

The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…

Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k

> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…

Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0

Thank you so much for sharing the link.

Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0

I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…

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Two EPIC Methylation Array Analysis Questions

How to get DMR for Infinium methylation EPIC v2

A: GEOquery Fails to Download Series Matrix File

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