Bioconductor Htseqtools

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780

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Deprecation chipseq htseqtools Bioconductor

updated 2.5 years ago by Basti ▴ 720 • written 2.5 years ago by Mick • 0

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2.9k

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htseqtools deseq2 counts cuffdiff

7.6 years ago Jon Bråte ▴ 250

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1.5k

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Coverage htSeqTools Coverage htSeqTools

updated 11.6 years ago by Valerie Obenchain ★ 6.8k • written 11.6 years ago by Juan L. Mateo ▴ 80

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1.5k

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GenomicRanges htSeqTools GenomicRanges htSeqTools

updated 11.6 years ago by Vincent J. Carey, Jr. 6.7k • written 11.6 years ago by Juan L. Mateo ▴ 80

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687

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IRanges htSeqTools IRanges htSeqTools

updated 11.7 years ago by Michael Lawrence 11k • written 11.7 years ago by Ian Donaldson ▴ 70

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827

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convert htSeqTools convert htSeqTools

11.7 years ago Oscar Reina ▴ 20

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1.1k

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htSeqTools ASSIGN htSeqTools ASSIGN

updated 11.7 years ago by Michael Lawrence 11k • written 11.7 years ago by Ian Donaldson ▴ 70

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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 …

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

Answer: Remove duplicates of colData in TreeSummarizedExperiment

Awards • All

Scholar to James W. MacDonald 63k