Biostar Batch Correction

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849

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scrna-seq integration batch correction

updated 3.2 years ago by Aaron Lun ★ 28k • written 3.2 years ago by p.joshi ▴ 40

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565

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methylation ComBat Linear models batch correction AIC

updated 3.3 years ago by Kevin Blighe 3.8k • written 3.3 years ago by lucasmiranda42 • 0

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376

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DESeq2 batch correction

updated 3.4 years ago by James W. MacDonald 62k • written 3.4 years ago by MT ▴ 10

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547

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Diffbind ATAC batch correction blocking factor

updated 3.6 years ago by Rory Stark ★ 4.6k • written 3.6 years ago by rm1238 • 0

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641

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deseq2 differential expression batch correction design

updated 3.8 years ago by Michael Love 39k • written 3.8 years ago by wunderl ▴ 40

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867

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deseq2 differential expression batch correction

updated 3.8 years ago by Michael Love 39k • written 3.8 years ago by wunderl ▴ 40

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1.2k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 4.0 years ago by Vladimir Kiselev ▴ 150 • written 4.0 years ago by hamza_karakurt ▴ 50

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Answer: Correct script for featurecounts in Rsubread by Gordon Smyth 47k

See - https://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html#quantifying-read-counts-for-eac…

Comment: Time-course, comparison of two groups by boczniak767 ▴ 720

Thank you very much @gordon-smyth ! I'm very happy that my test for interaction is okay. So I'll try to extend my test experiment to three …

Answer: Handling limma usage after running multiple imputation on the covariates with mi by Gordon Smyth 47k

limma is not designed to be used with multiply imputed covariates, so I can't offer a solution that uses the multiple imputes. Averaging t…

Answer: Correct script for featurecounts in Rsubread by James W. MacDonald 62k

Here's the relevant section from `?featureCounts` ``` Value: A list with the following components: counts: a data matrix c…

Comment: Can I run DESeq2 with SMART-Seq data by Assa Yeroslaviz ★ 1.5k

thanks, the filter is the other way around, true 🙈

Votes

A: gene dispersion, what does it mean?

Answer: gene dispersion, what does it mean?

Limma time series spline help

Answer: Correct script for featurecounts in Rsubread

Comment: Time-course, comparison of two groups

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