Bioconductor Gene set

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GAGE gene set go.gsets

updated 4.8 years ago by Luo Weijun ★ 1.6k • written 4.8 years ago by June. ▴ 10

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Gene set gene set analysis omiccircos

updated 7.8 years ago by yifangt ▴ 20 • written 10.4 years ago by Peter.Wood • 0

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globaltest gene set

8.4 years ago the_august • 0

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mroast roast gene set gene set analysis edgeR

updated 9.0 years ago by James W. MacDonald 68k • written 9.0 years ago by lattalic • 0

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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 …

Comment: Limma suqeezeVar by Mengchun • 0

Hi Gordon, Thank you for your reply. I'm working on a proteomics data imputation project, I would like to describe the intensity distribut…

Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0

thank you for your reply. I'm sorry if the question is off topic. the analysis and relative construction of the heatmap was done using bioc…

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

Without including the row names for the heatmap, it's impossible to know if the directionality is switched or not. Do note that the orderin…

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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