Bioconductor Rontotools

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KEGGREST ROntoTools KEGG KEGGgraph

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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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Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k

Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…

Comment: Sample-specific methylation values using QSEA by User3088 • 0

Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…

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…

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Unused arguments error without used arguments in GSVA?

Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte

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?

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