Bioconductor Batch correction

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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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1.5k

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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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1.3k

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deseq2 differential expression batch correction

updated 4.9 years ago by Michael Love 41k • written 4.9 years ago by wunderl ▴ 40

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998

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deseq2 differential expression batch correction design

updated 4.9 years ago by Michael Love 41k • written 4.9 years ago by wunderl ▴ 40

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977

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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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948

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.2k • written 4.7 years ago by rm1238 • 0

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613

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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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Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k

For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…

Comment: fgsea significant result by Chris • 0

Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…

Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0

Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k

The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…

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Handling multiple differential expression comparisons

Answer: fgsea significant result

package goseq seems to be not available on the latest version of R

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