Bioconductor ROntoTools

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KEGGREST ROntoTools KEGG KEGGgraph

2.4 years ago abf ▴ 30

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ROntoTools Rstudio bioconductor administratorIssues pathway analysis

9.3 years ago svlachavas ▴ 840

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Pathways ROntoTools Pathways ROntoTools

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Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools

updated 11.3 years ago by Paul Shannon ▴ 470 • written 11.3 years ago by enricoferrero ▴ 660

4 results • Page 1 of 1

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Comment: enrichGOgradient color change by lewis.roper • 0

I know you submitted this months ago but you're an absolute lifesaver mate, thank you

Comment: Warning message when running limma with covariates by Chris ▴ 20

Hi @gordonsmyth. Happy New Year! Wishing you all the best in 2025. Thank you so much for your kind support!

Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0

Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Votes

Answer: enrichGOgradient color change

How do I fix an odd voom plot in a combined dataset?

Answer: Warning message when running limma with covariates

A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

Awards • All

Scholar to Gordon Smyth 52k

Popular Question to James W. MacDonald 67k