Bioconductor Update

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224

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Versions Update BindingSiteFinder

updated 8 months ago by Mike Smith ★ 6.1k • written 8 months ago by M.Klostermann • 0

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993

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update Omixer maintainer

updated 2.8 years ago by shepherl 3.5k • written 2.8 years ago by l.j.sinke • 0

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990

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software error packages update

updated 3.2 years ago by James W. MacDonald 63k • written 3.2 years ago by bs14ab • 0

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2.5k

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biocmanager valid update packages

updated 3.4 years ago by Kevin Blighe 3.8k • written 3.4 years ago by bs14ab • 0

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533

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update new release version

4.0 years ago zzrickli • 0

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1.6k

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biocLite update all default ask

updated 4.6 years ago by Fischer-philipp ▴ 30 • written 4.6 years ago by rgiannico ▴ 10

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962

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PANTHER.db update annotation go

updated 4.6 years ago by Martin Morgan 25k • written 4.6 years ago by alfonsosaera • 0

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662

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support.bioconductor.org update News

4.7 years ago shepherl 3.5k

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783

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bioclite package installation update

6.6 years ago Malcolm Cook ★ 1.6k

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1.8k

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installation update

updated 6.6 years ago by James W. MacDonald 63k • written 6.6 years ago by debg • 0

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6.7k

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bioconductor biocupgrade upgrade update bioclite

7.4 years ago enricoferrero ▴ 660

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6.3k

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deseq2 update

8.7 years ago zshao1 • 0

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5.3k

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update bioclite

updated 8.9 years ago by Dan Tenenbaum ★ 8.2k • written 8.9 years ago by dianmante • 0

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1.3k

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experimentdata update

updated 9.0 years ago by Laurent Gatto 1.6k • written 9.0 years ago by paul.theodor.pyl ▴ 10

14 results • Page 1 of 1

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Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by James W. MacDonald 63k

No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …

Votes

Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Answer: Remove duplicates of colData in TreeSummarizedExperiment

Awards • All

Scholar to James W. MacDonald 63k