Bioconductor TCGA

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2.9k

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illimina 450k methylation qsea MEDIPS TCGA

updated 4 months ago by Matthias Lienhard ▴ 240 • written 7.1 years ago by justinburgener ▴ 20

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1.0k

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DESeq2 recount GTEx TCGA recount3

updated 12 months ago by ATpoint ★ 4.1k • written 12 months ago by David ▴ 20

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531

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recount3 TCGA RNASeq

updated 5 months ago by Leonardo Collado Torres ★ 1.0k • written 6 months ago by tangming2005 ▴ 190

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226

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TCGAbiolinks TCGA clinical TCGA-BRCA

written 7 weeks ago by BioinfoMug • 0

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504

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TCGA GenomicDataCommons GDC

written 10 months ago by António Miguel de Jesus Domingues ▴ 510

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494

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BatchEffect TCGA WGCNA

updated 10 months ago by ATpoint ★ 4.1k • written 10 months ago by khaserdene99 • 0

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GDCRNATools TCGA

7 days ago glaciya2018 • 0

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170

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TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data

9 weeks ago BioinfoMug • 0

8 results • Page 1 of 1

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Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70

Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …

Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k

> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…

Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0

Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…

Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k

There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …

Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k

MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…

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A: Error in DESeqDataSet : some values in assay are not integers

Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

SPIA plotP giving error

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Popular Question to rohitsatyam102 ▴ 20