Bioconductor Bsgenome

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BSgenome

updated 9 weeks ago by James W. MacDonald 65k • written 12 weeks ago by Kate • 0

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538

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OrgDb BSgenome

6 months ago • updated 12 weeks ago mat149 ▴ 70

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589

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SNPlocs BSgenome

written 6 months ago by Stevie Pederson • 0

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697

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intron BSgenome.Hsapiens.UCSC.hg38 BSgenome

updated 10 months ago by ATpoint ★ 4.1k • written 10 months ago by Lillian • 0

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962

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BSgenomeForge BSgenome

updated 10 months ago by James W. MacDonald 65k • written 10 months ago by kyliecode • 0

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bsgenome GenomicFeatures package

updated 11 months ago by Hervé Pagès 16k • written 11 months ago by Manish • 0

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862

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BSgenome

updated 3 months ago by eviatar.weizman • 0 • written 24 months ago by remerandmaxence ▴ 10

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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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