Bioconductor Batch correction

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619

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DESeq2 batch correction

updated 4.5 years ago by James W. MacDonald 65k • written 4.5 years ago by MT ▴ 10

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1.4k

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deseq2 differential expression batch correction

updated 4.9 years ago by Michael Love 42k • written 4.9 years ago by wunderl ▴ 40

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1.8k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.1 years ago by Vladimir Kiselev ▴ 150 • written 5.1 years ago by hamza_karakurt ▴ 50

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1.6k

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scrna-seq integration batch correction

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

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1.0k

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deseq2 differential expression batch correction design

updated 4.9 years ago by Michael Love 42k • written 4.9 years ago by wunderl ▴ 40

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954

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Diffbind ATAC batch correction blocking factor

updated 4.8 years ago by Rory Stark ★ 5.2k • written 4.8 years ago by rm1238 • 0

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988

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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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Comment: Ensembl plants at annotationHub? by Daniele • 0

Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele

Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30

Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…

Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0

Thanks a lot!

Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150

Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…

Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360

So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!

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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools

Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa

Rsubread counting peaks ATACseq

Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?

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