Bioconductor ROntoTools

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KEGGREST ROntoTools KEGG KEGGgraph

2.5 years ago abf ▴ 30

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ROntoTools Rstudio bioconductor administratorIssues pathway analysis

9.4 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 11.4 years ago by Paul Shannon ▴ 470 • written 11.4 years ago by enricoferrero ▴ 680

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Comment: input for singR function by iamin053 • 0

Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!

Comment: build samplesheet and plot profile by yf • 0

![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a

Answer: I am having issues with bowtie2_build by James W. MacDonald 67k

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…

Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k

Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…

Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Votes

A: Doubt about the "zero expression" genes or genes with no reads at all in the co

Answer: Unable to install nloptr

Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?

C: How does edgeR cpm function calculate log(CPM) values?

Answer: Selection of correct coefficients or contrasts in DESeq2

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