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How to place jplace Querries from EPA RAxML on the tree as branches in Teeio/ggtree?
treeio EPA jplace RAxML ggtree
8 months ago Vincent • 0
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How can I read in BEAST nexus tree with treeio and get all node values
treeio beast nexus ips OutbreakTools
3.0 years ago sknu003 • 0
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How to save changes on a phylogeneitc tree using ggtree and treeio?
ggtree treeio
3.4 years ago jdimopoulos21 • 0
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tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 3.8 years ago by ★ 1.2k • written 3.8 years ago by • 0
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Comment: tximport from Galaxy output by Pragathi • 0
@mikelove :Thank u
Comment: Can I use VST on TPM data? (DESeq2) by Michael Love 35k
The DESeq2 VST in `vst()` doesn't make sense on TPM because it is designed for NB distributed count data. The TPM are not close to NB (nega…
Comment: Can I use VST on TPM data? (DESeq2) by Bumble • 0
Hello again, Thank you very much for your reply. I had used rlog on the count data and got a good grouping on the sample heat map and an al…
Comment: Plot normalized expression or count values for a specific gene in limma by bioinformaticssrm2011 • 0
I am trying to use the same plot, but **norm** here is a count table where rows are gene name and column is a sample, how "**grouping**" fa…
Comment: tximport from Galaxy output by Michael Love 35k
See the tximport vignette, it explains all of this. I can't provide support for Galaxy here.
Votes
C: about paired-samples in edgeR
A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
Answer: Error with hclust
Filtering of RNA-seq data in EdgeR
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