Bioconductor Batch Correction

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2.4k

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scrna-seq integration batch correction

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by p.joshi ▴ 40

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1.9k

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methylation ComBat Linear models batch correction AIC

updated 6.2 years ago by Kevin Blighe ★ 4.0k • written 6.2 years ago by lucasmiranda42 • 0

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1.1k

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DESeq2 batch correction

updated 6.2 years ago by James W. MacDonald 68k • written 6.2 years ago by MT ▴ 10

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1.5k

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Diffbind ATAC batch correction blocking factor

updated 6.5 years ago by Rory Stark ★ 5.3k • written 6.5 years ago by rm1238 • 0

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1.5k

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deseq2 differential expression batch correction design

updated 6.7 years ago by Michael Love 43k • written 6.7 years ago by wunderl ▴ 40

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2.2k

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deseq2 differential expression batch correction

updated 6.7 years ago by Michael Love 43k • written 6.7 years ago by wunderl ▴ 40

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2.7k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.9 years ago by Vladimir Kiselev ▴ 150 • written 6.9 years ago by hamza_karakurt ▴ 60

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Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0

For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…

Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k

This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …

Comment: Bulk RNAseq analysis for by Mariami • 0

Thank you so much for your help! will try to proceed with the suggestion

Comment: Bulk RNAseq analysis for by Mariami • 0

Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…

Answer: Bulk RNAseq analysis for by Gordon Smyth 53k

All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…

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Comment: Are transformed values from rlog /vst log2 normalized counts?

Are transformed values from rlog /vst log2 normalized counts?

Answer: Bulk RNAseq analysis for

Answer: DiffBind differential analysis

Answer: Limma-voom sample weights and impact on DEG numbers

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