Bioconductor TCGAutils

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826

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normalization RNASEQ Normalization TCGAutils TCGA

updated 2.1 years ago by ATpoint ★ 4.6k • written 2.1 years ago by Deniz • 0

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2.2k

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MultiAssayExperiment curatedTCGAData TCGAutils

4.0 years ago svlachavas ▴ 840

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1.4k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.0 years ago by Marcel Ramos 700 • written 4.1 years ago by svlachavas ▴ 840

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1.5k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.0 years ago by Marcel Ramos 700 • written 4.2 years ago by svlachavas ▴ 840

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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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897

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TCGAutils

updated 5.7 years ago by Levi Waldron ★ 1.1k • written 5.7 years ago by vittorio.fortino • 0

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1.6k

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TCGAutils multiassayexperiment coad

updated 6.5 years ago by Marcel Ramos 700 • written 6.5 years ago by mario.zanfardino ▴ 160

7 results • Page 1 of 1

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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

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

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Votes

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

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