Bioconductor Dendrogram

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dendrogram hclust textanalysis R RStudio

4.8 years ago • updated 4.7 years ago Abby ▴ 10

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pheatmap hclust R dendrogram

8.7 years ago vd4mmind • 0

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complexheatmap heatmap.2 dendrogram dendextend heatmap

updated 9.2 years ago by jokergoo ▴ 200 • written 9.2 years ago by enricoferrero ▴ 680

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wgcna dendrogram network hclust

updated 11.3 years ago by Keith Hughitt ▴ 180 • written 11.3 years ago by Jon Bråte ▴ 270

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wgcna hclust plotdendroandcolors dendrogram

updated 11.3 years ago by James W. MacDonald 68k • written 11.3 years ago by Keith Hughitt ▴ 180

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Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k

There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…

Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0

@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…

Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0

Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …

Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k

Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …

Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20

You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…

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Answer: Clarification on counting in Rsubread (featureCounts)

Comment: Clarification on counting in Rsubread (featureCounts)

C: ControlGenes/ housekeeping genes Deseq2

Answer: Clarification on counting in Rsubread (featureCounts)

C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results

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Commentator to James W. MacDonald 68k

Great Question to fl ▴ 20

Popular Question to Lluís Revilla Sancho ▴ 760