Bioconductor Genomeintervals

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BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC

updated 11.1 years ago by Dan Tenenbaum ★ 8.2k • written 11.1 years ago by Wim Kreinen ▴ 100

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1.6k

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genomeintervals

updated 8.9 years ago by Nicolas Delhomme ▴ 320 • written 8.9 years ago by sjackman • 0

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genomeintervals UTRs exons CDS GenomicRanges

updated 6.8 years ago by Michael Lawrence ★ 11k • written 6.8 years ago by rubi ▴ 110

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granges bed genomicranges genomeintervals deseq2

6.3 years ago rbronste ▴ 60

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nclist genomeintervals

updated 8.3 years ago by Hervé Pagès 16k • written 8.3 years ago by Jurat Shahidin ▴ 80

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genomeIntervals

updated 8.9 years ago by Nicolas Delhomme ▴ 320 • written 9.1 years ago by mhz • 0

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Sequencing Annotation GO rtracklayer IRanges genomeIntervals Sequencing Annotation GO

14.3 years ago Robert Castelo ★ 3.3k

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920

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genomeIntervals genomeIntervals

updated 13.1 years ago by Hervé Pagès 16k • written 13.1 years ago by Julien Gagneur ▴ 50

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Annotation convert genomeIntervals Annotation convert genomeIntervals

12.2 years ago delhomme@embl.de ★ 1.2k

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119

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genomeIntervals GenomicRanges

5 weeks ago gshweta95 • 0

10 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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