Bioconductor Zinbwave

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edgeR DESeq2 single-cell scRNAseq zinbwave

updated 3.8 years ago by Aaron Lun ★ 28k • written 3.8 years ago by vincent.croset ▴ 20

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2.2k

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DESeq2 ZINB zinbwave deseq

updated 4.1 years ago by Michael Love 43k • written 4.1 years ago by rowcyclecamp • 0

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880

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zinbwave PCA

4.4 years ago Assa Yeroslaviz ★ 1.5k

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2.4k

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scRNA zinbwave batch IntegratedData

updated 4.5 years ago by davide risso ▴ 980 • written 4.5 years ago by Assa Yeroslaviz ★ 1.5k

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1.8k

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deseq2 zinbwave 10X scRNA-seq Differential expression

updated 4.6 years ago by Michael Love 43k • written 4.6 years ago by vincent.croset ▴ 20

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3.6k

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cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq

updated 4.7 years ago by davide risso ▴ 980 • written 4.7 years ago by Wagaa ▴ 10

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2.7k

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zinbwave deseq2 vegan

updated 5.3 years ago by James W. MacDonald 68k • written 5.3 years ago by zcbthug • 0

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1.3k

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deseq2 glm zinbwave ruvseq

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by Jakub ▴ 50

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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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