Bioconductor Isoforms

Showing : isoforms • reset

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isoforms DESeq2

3.0 years ago arfranco ▴ 130

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RATs RNA-Seq Isoforms DTU expression

updated 5.7 years ago by fruce_ki ▴ 20 • written 5.7 years ago by UserAnonyme • 0

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isoforms diffrential expression noncoding rna TSIS isoformswitchanalyzeR

6.8 years ago rbenel ▴ 40

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1.2k

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dexseq differential isoform usage isoforms summarizeoverlaps granges

6.9 years ago A ▴ 40

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1.7k

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cummerbund heatmap isoforms transcript_id

7.9 years ago domenico.somma • 0

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3.9k

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dexseq bitseq cuffdiff Differential exon usage isoforms

9.8 years ago • updated 9.7 years ago elle ▴ 10

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2.8k

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edgeR ruvseq rnaseq isoforms

9.8 years ago sergio.espeso-gil • 0

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1.6k

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DEXSeq transcripts isoforms

updated 9.8 years ago by Alejandro Reyes ★ 1.9k • written 9.8 years ago by peter_venhuizen • 0

8 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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