Bioconductor Batch correction

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2.0k

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scrna-seq integration batch correction

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by p.joshi ▴ 40

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1.4k

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methylation ComBat Linear models batch correction AIC

updated 5.3 years ago by Kevin Blighe ★ 4.0k • written 5.3 years ago by lucasmiranda42 • 0

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840

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DESeq2 batch correction

updated 5.4 years ago by James W. MacDonald 68k • written 5.4 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.6 years ago by Rory Stark ★ 5.2k • written 5.6 years ago by rm1238 • 0

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1.2k

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deseq2 differential expression batch correction design

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by wunderl ▴ 40

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1.8k

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deseq2 differential expression batch correction

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by wunderl ▴ 40

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2.3k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.0 years ago by Vladimir Kiselev ▴ 150 • written 6.0 years ago by hamza_karakurt ▴ 60

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Comment: Annotation package for Manduca sexta by GA ▴ 10

Thank you!

Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k

If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

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Looking for equivalent EPIC chip v1 vs. v2 annotation variables

Properly constructing a hypergeometric test

A: Is logFC a log2 fold change or some other base in scran::findMarkers

Comment: Error in retrieving clinical data

What is the cheapest day to fly on American Airlines? {Ask_Expert}

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