Bioconductor Vignette

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SummarizedExperiment vignette

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biomaRt vignette

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newpackage vignette installation

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flowcore vignette software error

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biocstyle vignette

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STRINGdb vignette

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software error cellmix vignette expressionset

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ggbio autoplot color vignette

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github vignette test developers

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vignette

updated 9.5 years ago by Dan Tenenbaum ★ 8.2k • written 9.5 years ago by KB ▴ 50

10 results • Page 1 of 1

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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…

Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k

Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…

Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0

Thank you so much ! It's working !

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k

Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…

Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k

Thanks @fep29! ^^

Votes

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

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Popular Question to Robert Castelo ★ 3.4k

Popular Question to Robert Ivanek ▴ 750