Bioconductor PCAtools

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5

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edgeR PCAtools

updated 26 days ago by Gordon Smyth 50k • written 28 days ago by Fabian • 0

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8

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DESeq2 RSTUDIO PCAtools

updated 1 day ago by swbarnes2 ★ 1.3k • written 3 days ago by Aaliya • 0

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2

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DESeq2 PCAtools

updated 3 hours ago by Michael Love 41k • written 1 day ago by Aaliya • 0

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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0

Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …

Answer: PCA plot suggestions by Michael Love 41k

For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

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