Bioconductor Batch Correction

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1.9k

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scrna-seq integration batch correction

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by p.joshi ▴ 40

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1.3k

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methylation ComBat Linear models batch correction AIC

updated 5.1 years ago by Kevin Blighe ★ 4.0k • written 5.1 years ago by lucasmiranda42 • 0

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789

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DESeq2 batch correction

updated 5.2 years ago by James W. MacDonald 67k • written 5.2 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.5 years ago by Rory Stark ★ 5.2k • written 5.5 years ago by rm1238 • 0

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1.1k

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deseq2 differential expression batch correction design

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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1.7k

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deseq2 differential expression batch correction

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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2.2k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.8 years ago by Vladimir Kiselev ▴ 150 • written 5.8 years ago by hamza_karakurt ▴ 60

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Answer: Unable to find sample sheet file for ChAMP methylation data analysis by James W. MacDonald 67k

There is an example file in the extdata directory of the `minfiData` package that you could emulate.

Comment: Rain error: invalid annotation of time points by Dominik • 0

Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…

Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k

Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…

Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0

I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10

Thank you so much for taking time to provide this clarification!

Votes

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

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