Bioconductor TCGAutils

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TCGAutils

updated 8 days ago by James W. MacDonald 67k • written 8 days ago by xiaofeiwang18266 ▴ 50

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862

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normalization RNASEQ Normalization TCGAutils TCGA

updated 2.2 years ago by ATpoint ★ 4.6k • written 2.2 years ago by Deniz • 0

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2.2k

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MultiAssayExperiment curatedTCGAData TCGAutils

4.1 years ago svlachavas ▴ 840

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1.4k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.1 years ago by Marcel Ramos 700 • written 4.1 years ago by svlachavas ▴ 840

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1.6k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.1 years ago by Marcel Ramos 700 • written 4.3 years ago by svlachavas ▴ 840

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4.7k

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 5.5 years ago by Marcel Ramos 700 • written 5.5 years ago by Dario Strbenac ★ 1.5k

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909

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TCGAutils

updated 5.8 years ago by Levi Waldron ★ 1.1k • written 5.8 years ago by vittorio.fortino • 0

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TCGAutils multiassayexperiment coad

updated 6.6 years ago by Marcel Ramos 700 • written 6.6 years ago by mario.zanfardino ▴ 160

8 results • Page 1 of 1

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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…

Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k

Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…

Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0

Thank you so much ! It's working !

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k

Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…

Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k

Thanks @fep29! ^^

Votes

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

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Popular Question to Robert Castelo ★ 3.4k

Popular Question to Robert Ivanek ▴ 750