Bioconductor Shrinkage

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shrinkage DifferentialExpression DESeq2

updated 15 months ago by ATpoint ★ 4.5k • written 15 months ago by Abir.khazaal ▴ 10

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1.1k

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shrinkage apeglm

2.5 years ago Frederik Ziebell ▴ 30

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2.8k

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deseq2 shrinkage

updated 24 months ago by Michael Love 42k • written 4.7 years ago by Nicolas Rosewick ▴ 20

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1.3k

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deseq2 shrinkage

updated 5.8 years ago by Michael Love 42k • written 5.8 years ago by vvi • 0

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4.3k

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deseq2 betaPrior shrinkage significance

6.5 years ago brynedal ▴ 40

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1.5k

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deseq2 log2fc shrinkage

updated 6.9 years ago by Michael Love 42k • written 6.9 years ago by aec ▴ 90

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Comment: ESTMATE, MCPcounter, EPIC, xCell input by Kang • 0

These are not, as far as I know, bioconductor packages. You should query on the websites for those specific software programs. @[mapquest][…

Comment: Robust way of dealing with low number of samples for Differential Gene Expressio by Kang • 0

I believe that pseudo-bulking is a strong way to approach DE, as long as it is possible to reliably identify the cell type across data and …

Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0

Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…

Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k

> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…

Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0

I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…

Votes

A: Up/Down Regulated GeneList from edgeR and R

A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis

Answer: Combining RNAseq and microarray data using edgeR/limma-voom

Answer: How do I merge a list of GRanges?

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Teacher to Gordon Smyth 51k

Popular Question to Guido Hooiveld ★ 4.1k