Bioconductor Narrowpeaks

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 10.0 years ago by Gordon Smyth 52k • written 10.0 years ago by samuel collombet ▴ 140

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Rsubread atac-seq narrowpeaks featurecounts

updated 7.5 years ago by Wei Shi ★ 3.6k • written 7.5 years ago by j.bergenstrahle ▴ 90

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GO DiffBind NarrowPeaks GO DiffBind NarrowPeaks

11.3 years ago Rory Stark ★ 5.2k

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ChIPSeq chipseq NarrowPeaks ChIPSeq chipseq NarrowPeaks

11.1 years ago Robert Chase ▴ 10

4 results • Page 1 of 1

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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10

It worked, I think I finally understand and accept that fact. Sorry and thank you again !

Comment: parameters of filterByExpr by Gordon Smyth 52k

You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…

Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k

modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…

Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k

Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…

Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k

`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …

Votes

Answer: LogFC values in edgeR - w/wo intercept

How to formulate 2 factor nested design in DESeq2

Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm

Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)

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