Bioconductor Splicing

Showing : splicing • reset

votes

751

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splicing limma edgeR

updated 11 months ago by Gordon Smyth 52k • written 11 months ago by scoops_streams_06 • 0

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747

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transcriptome splicing assembly

updated 2.3 years ago by James W. MacDonald 68k • written 2.3 years ago by Marianna ▴ 20

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1.2k

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splicing Exon featureCounts subread DEXSeq

2.8 years ago NIK • 0

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912

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psichomics SUPPA Splicing Alternative Splicing Retained Introns

4.4 years ago noahhelton98 ▴ 20

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3.1k

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edger normalization differential exon usage splicing

updated 4.4 years ago by Yunshun Chen ▴ 900 • written 4.4 years ago by oakhamwolf • 0

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1.5k

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DEXSeq Splicing Exon Usage

5.1 years ago gunjan.dikshit • 0

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1.3k

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ciri splicing splicesites

updated 5.1 years ago by lhddiallo • 0 • written 6.8 years ago by csijst • 0

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1.0k

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junctionseq splicing RNAseq DEXSeq

5.3 years ago stuart ▴ 10

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1.8k

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genomicalignments splicing coverage

updated 5.4 years ago by Michael Lawrence ★ 11k • written 7.9 years ago by rasi1983 ▴ 10

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1.1k

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dexseq splicing sqtl qtl

updated 6.1 years ago by Alejandro Reyes ★ 1.9k • written 6.1 years ago by rtunney2 • 0

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2.1k

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deseq2 splicing

updated 6.8 years ago by Michael Love 43k • written 6.8 years ago by yannickwurm • 0

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1.8k

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DRIMSeq splicing differential isoform usage

updated 8.1 years ago by Gosia Nowicka ▴ 90 • written 8.1 years ago by kristoffer.vittingseerup ▴ 20

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3.2k

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sgseq splicing alternative splicing

updated 9.0 years ago by Leonard Goldstein ▴ 260 • written 9.0 years ago by vakul.mohanty ▴ 20

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2.0k

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microarray splicing

updated 9.1 years ago by Sonika Tyagi ▴ 20 • written 10.4 years ago by gv ▴ 40

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1.7k

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DEXSeq splicing python SAM

9.4 years ago Fiona ▴ 70

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2.5k

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SGSeq analyzeFeatures Splicing

10.2 years ago Paolo Guarnieri ▴ 20

16 results • Page 1 of 1

Recent ...

Replies

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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