Bioconductor Update

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770

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Versions Update BindingSiteFinder

updated 2.1 years ago by Mike Smith ★ 6.6k • written 2.1 years ago by M.Klostermann • 0

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1.7k

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update Omixer maintainer

updated 4.2 years ago by shepherl 4.1k • written 4.2 years ago by l.j.sinke • 0

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1.7k

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software error packages update

updated 4.6 years ago by James W. MacDonald 68k • written 4.6 years ago by bs14ab • 0

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3.6k

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biocmanager valid update packages

updated 4.8 years ago by Kevin Blighe ★ 4.0k • written 4.8 years ago by bs14ab • 0

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873

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update new release version

5.5 years ago zzrickli • 0

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2.6k

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biocLite update all default ask

updated 6.0 years ago by Fischer-philipp ▴ 30 • written 6.0 years ago by rgiannico ▴ 10

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1.4k

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PANTHER.db update annotation go

updated 6.1 years ago by Martin Morgan 25k • written 6.1 years ago by alfonsosaera • 0

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959

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support.bioconductor.org update News

6.2 years ago shepherl 4.1k

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1.0k

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bioclite package installation update

8.0 years ago Malcolm Cook ★ 1.6k

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2.2k

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installation update

updated 8.1 years ago by James W. MacDonald 68k • written 8.1 years ago by debg • 0

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7.3k

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bioconductor biocupgrade upgrade update bioclite

8.8 years ago enricoferrero ▴ 680

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6.8k

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deseq2 update

10.2 years ago zshao1 • 0

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5.8k

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update bioclite

updated 10.3 years ago by Dan Tenenbaum ★ 8.2k • written 10.3 years ago by dianmante • 0

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1.8k

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experimentdata update

updated 10.4 years ago by Laurent Gatto 1.6k • written 10.4 years ago by paul.theodor.pyl ▴ 10

14 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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