Bioconductor Recountworkflow

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recount recountWorkflow recount3

updated 2.0 years ago by Leonardo Collado Torres ★ 1.1k • written 2.4 years ago by dml • 0

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recountWorkflow recount3

updated 2.3 years ago by Leonardo Collado Torres ★ 1.1k • written 2.4 years ago by soever ▴ 20

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recount recountWorkflow recount3

updated 2.0 years ago by Leonardo Collado Torres ★ 1.1k • written 2.4 years ago by Max Bone • 0

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recount3 recountWorkflow

updated 3.5 years ago by Leonardo Collado Torres ★ 1.1k • written 3.6 years ago by António Miguel de Jesus Domingues ▴ 510

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Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k

Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.

Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k

The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…

Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0

I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…

Answer: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k

Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …

Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0

It is in ! It just took longer than planned :) ... aaaand now that I added the heatmap in I realize lits of genes really do not look like t…

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Comment: Heatmap of a transformed deseq object with pheatmap

DESeq2: Question about the alpha in summary() and results()

Comment: How to load scRNA-seq data from GEO

limma correction for tumor purity

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