Bioconductor TCGAutils

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normalization RNASEQ Normalization TCGAutils TCGA

updated 24 months ago by ATpoint ★ 4.5k • written 24 months ago by Deniz • 0

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2.1k

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MultiAssayExperiment curatedTCGAData TCGAutils

4.0 years ago svlachavas ▴ 830

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1.4k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.0 years ago by Marcel Ramos 700 • written 4.0 years ago by svlachavas ▴ 830

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1.5k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.0 years ago by Marcel Ramos 700 • written 4.1 years ago by svlachavas ▴ 830

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4.6k

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 5.4 years ago by Marcel Ramos 700 • written 5.4 years ago by Dario Strbenac ★ 1.5k

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890

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TCGAutils

updated 5.6 years ago by Levi Waldron ★ 1.1k • written 5.6 years ago by vittorio.fortino • 0

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1.6k

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TCGAutils multiassayexperiment coad

updated 6.4 years ago by Marcel Ramos 700 • written 6.4 years ago by mario.zanfardino ▴ 160

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Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by Paul • 0

You are an absolute lifesaver, thank you so much for the clarification!

Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k

The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…

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)

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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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