Bioconductor Batch Correction

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.7 years ago by Vladimir Kiselev ▴ 150 • written 5.7 years ago by hamza_karakurt ▴ 60

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1.6k

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deseq2 differential expression batch correction

updated 5.5 years ago by Michael Love 43k • written 5.5 years ago by wunderl ▴ 40

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1.1k

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deseq2 differential expression batch correction design

updated 5.5 years ago by Michael Love 43k • written 5.5 years ago by wunderl ▴ 40

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1.1k

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Diffbind ATAC batch correction blocking factor

updated 5.3 years ago by Rory Stark ★ 5.2k • written 5.3 years ago by rm1238 • 0

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768

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DESeq2 batch correction

updated 5.1 years ago by James W. MacDonald 67k • written 5.1 years ago by MT ▴ 10

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1.2k

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methylation ComBat Linear models batch correction AIC

updated 5.0 years ago by Kevin Blighe ★ 4.0k • written 5.0 years ago by lucasmiranda42 • 0

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1.8k

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scrna-seq integration batch correction

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by p.joshi ▴ 40

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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…

Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…

Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k

Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …

Comment: fail to use addPerROIQC in Rmd by liu.n • 0

That's odd. So it can run successfully within markdown but would be failed when knitting?

Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0

> dim(spe) [1] 19962 425

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Answer: contrast matrix design for a continuous variable

A: What's the difference between p.adjust and qvalue?

Answer: DESeq2- merging technical vs biological replicates

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

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