Bioconductor Htseqtools

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Deprecation chipseq htseqtools Bioconductor

updated 4.5 years ago by Basti ▴ 780 • written 4.5 years ago by Mick • 0

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4.2k

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htseqtools deseq2 counts cuffdiff

9.6 years ago Jon Bråte ▴ 270

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2.2k

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Coverage htSeqTools Coverage htSeqTools

updated 13.5 years ago by Valerie Obenchain ★ 6.8k • written 13.6 years ago by Juan L. Mateo ▴ 80

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1.9k

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GenomicRanges htSeqTools GenomicRanges htSeqTools

updated 13.6 years ago by Vincent J. Carey, Jr. 6.7k • written 13.6 years ago by Juan L. Mateo ▴ 80

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1.0k

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IRanges htSeqTools IRanges htSeqTools

updated 13.6 years ago by Michael Lawrence ★ 11k • written 13.6 years ago by Ian D. ▴ 70

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convert htSeqTools convert htSeqTools

13.6 years ago Oscar Reina ▴ 20

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1.5k

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htSeqTools ASSIGN htSeqTools ASSIGN

updated 13.6 years ago by Michael Lawrence ★ 11k • written 13.6 years ago by Ian D. ▴ 70

7 results • Page 1 of 1

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Answer: ROAST compare results with complex design by James W. MacDonald 68k

You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k

Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200

I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k

Not sure I understand. You ask how to do something and then show how one would do so.

Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10

Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…

Votes

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi

Can NanoString data be analyzed using DESeq2?

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