Bioconductor Tcgautils

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normalization RNASEQ Normalization TCGAutils TCGA

updated 16 months ago by ATpoint ★ 4.0k • written 16 months ago by Deniz • 0

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1.8k

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MultiAssayExperiment curatedTCGAData TCGAutils

3.4 years ago svlachavas ▴ 830

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1.2k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 3.4 years ago by Marcel Ramos 690 • written 3.4 years ago by svlachavas ▴ 830

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1.3k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 3.4 years ago by Marcel Ramos 690 • written 3.5 years ago by svlachavas ▴ 830

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3.8k

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 4.8 years ago by Marcel Ramos 690 • written 4.8 years ago by Dario Strbenac ★ 1.5k

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763

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TCGAutils

updated 5.1 years ago by Levi Waldron ★ 1.1k • written 5.1 years ago by vittorio.fortino • 0

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1.3k

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TCGAutils multiassayexperiment coad

updated 5.8 years ago by Marcel Ramos 690 • written 5.8 years ago by mario.zanfardino ▴ 160

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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

How am i making the data? I am using the DESeq2 output data which I had generated

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k

Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …

Answer: Citation for edgeR user guide by Gordon Smyth 50k

Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You are just making up data? What is the point of this exercise?

Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k

What do you mean by 'the information'? Do you have things in particular that you want?

Votes

Answer: Citation for edgeR user guide

Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)

Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.

Answer: minfi::read.metharray.exp

Comment: Trying to use enrichGO

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