Bioconductor Biotype

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ssgsea GSVA biotype proteincoding msigdb

updated 11 months ago by tifaGis • 0 • written 21 months ago by snijesh ▴ 200

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2.1k

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grch37 transcripts biotype biomaRt ncrna

updated 7.0 years ago by James W. MacDonald 68k • written 7.1 years ago by sergio.martinezcuesta ▴ 10

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2.3k

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DESeq2 PCA rlog transformation biotype

7.4 years ago JoannaF ▴ 10

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1.3k

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scater sce biotype R

updated 7.5 years ago by Aaron Lun ★ 29k • written 7.5 years ago by thebadpenny • 0

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1.7k

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biomart TF biotype ensembl mus musculus

updated 7.6 years ago by Mike Smith ★ 6.6k • written 7.6 years ago by rbronste ▴ 60

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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…

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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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