Bioconductor Batch correction

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2.0k

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scrna-seq integration batch correction

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by p.joshi ▴ 40

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1.5k

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methylation ComBat Linear models batch correction AIC

updated 5.4 years ago by Kevin Blighe ★ 4.0k • written 5.4 years ago by lucasmiranda42 • 0

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869

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DESeq2 batch correction

updated 5.5 years ago by James W. MacDonald 68k • written 5.5 years ago by MT ▴ 10

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1.3k

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Diffbind ATAC batch correction blocking factor

updated 5.8 years ago by Rory Stark ★ 5.2k • written 5.8 years ago by rm1238 • 0

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1.2k

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deseq2 differential expression batch correction design

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by wunderl ▴ 40

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1.9k

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deseq2 differential expression batch correction

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by wunderl ▴ 40

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2.4k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.1 years ago by Vladimir Kiselev ▴ 150 • written 6.1 years ago by hamza_karakurt ▴ 60

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Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0

Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…

Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0

The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …

Comment: parameters of filterByExpr by Paul Harrison ▴ 110

It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k

voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0

Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…

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A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

Answer: GAlignments Cigar to GRanges

parameters of filterByExpr

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Scholar to James W. MacDonald 68k