Bioconductor Macs

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medip_seq Macs

4.8 years ago Mar Mar ▴ 20

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Chip Seq Histone H3K27me3 macs diffbind

5.3 years ago researcher • 0

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atac-seq diffbind macs2 macs peak finding

updated 7.8 years ago by BioinfGuru ▴ 70 • written 8.4 years ago by igor ▴ 50

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p-value medips MACS

updated 9.6 years ago by Lukas Chavez ▴ 570 • written 9.6 years ago by tptacek3050 • 0

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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…

Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k

I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…

Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…

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C: How does edgeR cpm function calculate log(CPM) values?

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis

scater/scran with TPMs from Salmon - counts?

A: Full length single-cell RNA-seq - tximport output for downstream analysis

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