Bioconductor Variantfiltering

Showing : variantfiltering • reset

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1.4k

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bioconductor variantfiltering

6.7 years ago Claus.Hultschig • 0

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variantannotation variantfiltering

updated 7.1 years ago by Michael Lawrence ★ 11k • written 7.1 years ago by Bogdan ▴ 670

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366

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VariantFiltering

updated 10 months ago by Robert Castelo ★ 3.3k • written 10 months ago by Andrew Beggs ▴ 90

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1.1k

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VariantFiltering

8.8 years ago claire.simpson • 0

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1.5k

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RNAseq123 VariantFiltering Alignment VariantAnnotation

updated 18 months ago by James W. MacDonald 65k • written 18 months ago by Mohamed ▴ 30

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variantfiltering phastcons

updated 9.0 years ago by Robert Castelo ★ 3.3k • written 9.0 years ago by Stefanie Tauber ▴ 40

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455

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VariantAnnotation VariantFiltering

7 months ago Bogdan ▴ 670

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1.5k

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sequencing transcription variantfiltering annotation News

8.9 years ago Matthew Ritchie ▴ 1000

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1.7k

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VariantFiltering VariantFiltering

10.0 years ago Robert Castelo ★ 3.3k

9 results • Page 1 of 1

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

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…

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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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