Bioconductor Medip-seq

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696

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R medip-seq MEDIPS

21 months ago Luomeng • 0

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2.0k

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MEDIP-seq CNV TCGA450KHumanMethylationCalibrationDataset qsea PRAD

3.5 years ago rtrivedi1 ▴ 10

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1.5k

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MEDIPS MeDIP-seq

updated 3.2 years ago by Lukas ▴ 20 • written 5.0 years ago by lshepard ▴ 40

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879

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medip-seq createset

updated 5.9 years ago by Bioconductor Community 0 • written 6.0 years ago by oussama.badad • 0

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1.1k

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medips medip-seq dna methylation dmr analysis

updated 6.0 years ago by Lukas Chavez ▴ 570 • written 6.0 years ago by mtefit • 0

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946

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medip-seq methylation CpGs

6.0 years ago saripalligautam86 ▴ 10

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2.2k

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medips bsgenome medip-seq

updated 6.7 years ago by Lukas Chavez ▴ 570 • written 6.7 years ago by vjain • 0

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7.6k

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diffbind medip-seq edger deseq2

updated 11 weeks ago by khanwaled68 • 0 • written 8.7 years ago by florian.noack ▴ 60

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2.1k

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R medips medip-seq

8.3 years ago • updated 7.4 years ago stb • 0

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1.9k

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medips medip-seq error lukas

updated 7.5 years ago by Matthias Lienhard ▴ 280 • written 7.5 years ago by anupriyaverma1408 • 0

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1.4k

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medips medip-seq peak finding luckas

updated 7.5 years ago by Lukas Chavez ▴ 570 • written 7.5 years ago by anupriyaverma1408 • 0

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1.3k

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medips R medip-seq pair-end reads

updated 8.0 years ago by Lukas Chavez ▴ 570 • written 8.0 years ago by stb • 0

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1.2k

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medips medip-seq R pair-end reads

updated 8.2 years ago by Lukas Chavez ▴ 570 • written 8.2 years ago by stb • 0

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1.7k

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R medip-seq medips bwa

updated 8.3 years ago by Lukas Chavez ▴ 570 • written 8.3 years ago by stb • 0

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1.5k

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annotation chippeakanno rattus norvegicus medip-seq

8.7 years ago Vang Le ▴ 80

15 results • Page 1 of 1

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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