Bioconductor Differential expression analysis

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EdgeR differential expression analysis covariates

updated 4.4 years ago by Gordon Smyth 52k • written 4.4 years ago by Lucy ▴ 60

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980

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EdgeR edgeR RNA-seq differential expression analysis blocking factors

updated 4.4 years ago by Gordon Smyth 52k • written 4.4 years ago by Lucy ▴ 60

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2.1k

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deseq2 mirdeep2 microRNA differential expression analysis

updated 4.6 years ago by Michael Love 43k • written 4.6 years ago by ljbond • 0

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845

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microarray differential expression analysis GPL2025 affymetrix

updated 5.7 years ago by Aaron Lun ★ 28k • written 5.7 years ago by pratikshasharma47 • 0

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6.9k

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deseq2 scRNA-Seq RNA-Seq differential expression analysis

updated 5.7 years ago by Michael Love 43k • written 5.7 years ago by hamza_karakurt ▴ 60

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3.9k

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deseq2 rna-seq differential expression analysis

5.8 years ago shreygandhi1990 ▴ 10

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1.5k

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differential expression analysis ballgown r batch effects total number of reads

updated 6.2 years ago by James W. MacDonald 67k • written 6.2 years ago by amy16 • 0

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Answer: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

I haven't used nf-core but, from browsing through their documentation, they didn't seem to have any pipeline for differential transcript ex…

Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k

Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…

Comment: athPkgBuilder data source :missing probesets by bobihanigujjar • 0

In this article, we'll explore the demand for unbranded BJJ Gis and the benefits of choosing unbranded Gis for customization. [does anyone …

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Transcript-level differential expression using DESeq2

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

Comment: ANOVA like approach of edgeR

Comment: Crossover design with limma

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