Bioconductor Tophat

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1.1k

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snpeff python tophat r RNAseq123

updated 3.6 years ago by Kevin Blighe ★ 4.0k • written 3.6 years ago by kusum • 0

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1.1k

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noiseq rsubread tophat bowtie bowtie2

5.7 years ago Marcelo Laia ▴ 450

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1.1k

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topGO tophat kolmogorov-smirnov test

updated 7.6 years ago by James W. MacDonald 68k • written 7.6 years ago by aaronrosenstein • 0

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2.5k

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R rnaseq tophat summarizeoverlaps systempiper

updated 8.3 years ago by Thomas Girke ★ 1.7k • written 8.3 years ago by abass.conteh • 0

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8.2k

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deseq deseq2 edger tophat bowtie

9.7 years ago ysdel ▴ 40

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2.7k

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rnaseq summarizeOverlaps deseq2 tophat genomicalignments

updated 10.3 years ago by Dan Tenenbaum ★ 8.2k • written 10.3 years ago by alejandro.colaneri ▴ 20

6 results • Page 1 of 1

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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