Bioconductor Bed

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readTranscriptFeatures R genomation bed

updated 15 months ago by James W. MacDonald 65k • written 15 months ago by sat • 0

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bed bigBed rtracklayer ucsc

17 months ago L ▴ 50

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rtracklayer R bed

updated 16 months ago by Walters • 0 • written 21 months ago by L ▴ 50

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mappability bed python

updated 2.3 years ago by James W. MacDonald 65k • written 2.3 years ago by the • 0

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rtracklayer bed

updated 3.2 years ago by merv ▴ 120 • written 8.1 years ago by Ryan C. Thompson ★ 7.9k

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rtracklayer bed genomicranges

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5.6 years ago maltethodberg ▴ 180

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bed vcf

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granges bed genomicranges genomeintervals deseq2

6.3 years ago rbronste ▴ 60

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rtracklayer bed software error

updated 6.6 years ago by Michael Lawrence ★ 11k • written 6.6 years ago by Ryan C. Thompson ★ 7.9k

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coverage bed

updated 6.7 years ago by James W. MacDonald 65k • written 6.7 years ago by sgupt46 • 0

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annotationhub bugs encode bed

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rtracklayer import bed

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gviz BED Ucsc UcscTrack

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rtracklayer NA BED getseq

8.5 years ago Dimitris Polychronopoulos ▴ 80

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readvcf plink file conversion bed bioc-devel

9.1 years ago mjsduncan • 0

16 results • Page 1 of 1

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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: 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

A: Print Differentially Expressed Exons From Dexseq Results

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