Bioconductor Tcgautils

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610

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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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1.2k

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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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755

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TCGAutils

updated 5.0 years ago by Levi Waldron ★ 1.1k • written 5.0 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: what is the sampleFiles by James W. MacDonald 65k

I don't see any sampleFiles argument for any function in that package. Ideally you would at least tell us what function you are using.

Comment: Interaction Terms in DESeq2 - Shrinkage by Michael Love 41k

Yes, apeglm requires relevel and nbinomWaldTest to generate the coefficient estimate and its SE. Alternatively you can use ashr with a con…

Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0

Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…

Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690

If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…

Comment: Memory errors using read.bismark? by Juan Higareda • 0

Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…

Votes

Comment: Not fully paired differential gene expression analysis

Comment: [DiffBind] Obtaining normalization factors

Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var

Comment: Not fully paired differential gene expression analysis

Answer: GSVA error

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