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Are equal whisker lengths important in an RLE plot?
EDASeq EDA
17 months ago BioinfGuru ▴ 70
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4
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
22 months ago samuel.channon • 0
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4
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2.6k
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Comparing discrete variable to PCA
EDA pcaExplorer PCAtools PCA
updated 4.1 years ago by ▴ 20 • written 5.4 years ago by ▴ 120
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5
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2.5k
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Paired design, normalisation and batch effects.
deseq2 eda sva rna-seq
updated 9.4 years ago by ▴ 610 • written 9.4 years ago by ▴ 10
4 results • Page 1 of 1
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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