Bioconductor MACS

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medip_seq Macs

5.5 years ago Mar Mar ▴ 20

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Chip Seq Histone H3K27me3 macs diffbind

6.0 years ago researcher • 0

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atac-seq diffbind macs2 macs peak finding

updated 8.5 years ago by BioinfGuru ▴ 70 • written 9.0 years ago by igor ▴ 50

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p-value medips MACS

updated 10.3 years ago by Lukas Chavez ▴ 570 • written 10.3 years ago by tptacek3050 • 0

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Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k

What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…

Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0

Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…

Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

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Answer: Limpa Pipeline Order

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

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Popular Question to Assa Yeroslaviz ★ 1.5k