Bioconductor Batch correction

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1.5k

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scrna-seq integration batch correction

updated 4.2 years ago by Aaron Lun ★ 28k • written 4.3 years ago by p.joshi ▴ 40

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956

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methylation ComBat Linear models batch correction AIC

updated 4.4 years ago by Kevin Blighe ★ 3.9k • written 4.4 years ago by lucasmiranda42 • 0

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605

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DESeq2 batch correction

updated 4.4 years ago by James W. MacDonald 65k • written 4.4 years ago by MT ▴ 10

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928

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.1k • written 4.7 years ago by rm1238 • 0

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980

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deseq2 differential expression batch correction design

updated 4.8 years ago by Michael Love 41k • written 4.8 years ago by wunderl ▴ 40

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1.3k

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deseq2 differential expression batch correction

updated 4.8 years ago by Michael Love 41k • written 4.8 years ago by wunderl ▴ 40

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1.7k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.0 years ago by Vladimir Kiselev ▴ 150 • written 5.0 years ago by hamza_karakurt ▴ 50

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Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k

I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …

Comment: Theoretical WGCNA Question by Garrett • 0

Thanks Peter!

Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0

Thank you!

Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240

They are reorder in the decreasing order.

Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0

Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…

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Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

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