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DifferentialExpression DESeq2 tidybulk RNASeq

1 day ago s.malik • 0

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DESeq2 designmatrix edgeR limma tidybulk

updated 2.3 years ago by Michael Love 43k • written 2.3 years ago by aditya.m ▴ 10

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edgeR R tidyverse tidybulk

2.5 years ago Amit Indap ▴ 10

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Comment: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm by Charles • 0

I am trying this but it is slow. Actually it may be better to just make a VCF file with the appropriate tools and only then load it? ``` …

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 …

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Comment: How to load scRNA-seq data from GEO

limma correction for tumor purity

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