Bioconductor TCGAutils

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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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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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1.5k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.1 years ago by Marcel Ramos 700 • written 4.2 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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902

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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

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Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0

Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

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

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