Package: ROntoTools 2.35.0

Sorin Draghici

ROntoTools: R Onto-Tools suite

Suite of tools for functional analysis.

Authors:Calin Voichita <[email protected]> and Sahar Ansari <[email protected]> and Sorin Draghici <[email protected]>

ROntoTools_2.35.0.tar.gz
ROntoTools_2.35.0.zip(r-4.5)ROntoTools_2.35.0.zip(r-4.4)ROntoTools_2.35.0.zip(r-4.3)
ROntoTools_2.35.0.tgz(r-4.4-any)ROntoTools_2.35.0.tgz(r-4.3-any)
ROntoTools_2.35.0.tar.gz(r-4.5-noble)ROntoTools_2.35.0.tar.gz(r-4.4-noble)
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ROntoTools.pdf |ROntoTools.html✨
ROntoTools/json (API)
NEWS

# Install 'ROntoTools' in R:
install.packages('ROntoTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:ROntoTools-2.35.0(bioc 3.21)ROntoTools-2.34.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

networkanalysismicroarraygraphsandnetworks

5.10 score 2 packages 15 scripts 364 downloads 7 mentions 15 exports 28 dependencies

Last updated 2 months agofrom:d2b826dab2. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winWARNINGNov 30 2024
R-4.5-linuxWARNINGNov 30 2024
R-4.4-winWARNINGNov 30 2024
R-4.4-macWARNINGNov 30 2024
R-4.3-winWARNINGNov 30 2024
R-4.3-macWARNINGNov 30 2024

Exports:alpha1MRalphaMLGcompute.fishercompute.normalInvkeggPathwayGraphskeggPathwayNamesnodeWeightspDispepeEdgeRenderInfopeNodeRenderInfoplotsetEdgeWeightssetNodeWeightsSummary

Dependencies:askpassBiocGenericsBiostringsbitopsbootcrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatagraphhttrIRangesjsonliteKEGGgraphKEGGRESTmimeopensslpngR6RCurlRgraphvizS4VectorssysUCSC.utilsXMLXVectorzlibbioc

ROntoTools

Rendered fromrontotools.Rnwusingutils::Sweaveon Nov 30 2024.

Last update: 2016-04-15
Started: 2013-03-22

Readme and manuals

Help Manual

Help pageTopics
Compute alpha weightsalpha1MR
Compute alpha weightsalphaMLG
Combine independent p-values using the Fisher methodcompute.fisher
Combine independent p-values using the normal inversion methodcompute.normalInv
Download and parse KEGG pathway datakeggPathwayGraphs
Obtain KEGG pathway titleskeggPathwayNames
Retrieve the node weights of a graphnodeWeights nodeWeights,graph,character-method nodeWeights,graph,missing-method nodeWeights,graph,numeric-method
Primary dis-regulation: Pathway analysis approach based on the unexplained dis-regulation of genespDis
Class that encodes the result of pDis analysis for a single pathwaypDisPathway-class
Primary dis-regulation (pDis) result classpDisRes-class
Pathway-Express: Pathway analysis of signaling pathwayspe
Extract edge render information from a 'pePathway-class' objectpeEdgeRenderInfo
Extract node render information from a 'pePathway-class' objectpeNodeRenderInfo
Class that encodes the result of Pathway-Express for a single pathwaypePathway-class
Pathway-Express result classpeRes-class
Plot pathway level statisticsplot,pePathway,character-method plot,pePathway,missing-method
Plot Pathway-Express resultplot,peRes,character-method plot,peRes,missing-method
Set gene weights based on edge typesetEdgeWeights
Set node weightssetNodeWeights
Summarize the results of a Pathway-Express analysisSummary,pDisRes-method
Summarize the results of a Pathway-Express analysisSummary,peRes-method
Summarize the results of a primary dis-regulation (pDis) analysissummary.pDisRes
Summarize the results of a Pathway-Express analysissummary.peRes