Package: ROntoTools 2.41.0

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_2.41.0.tar.gz
ROntoTools_2.41.0.zip(r-4.7)ROntoTools_2.41.0.zip(r-4.6)ROntoTools_2.41.0.zip(r-4.5)
ROntoTools_2.41.0.tgz(r-4.6-any)ROntoTools_2.41.0.tgz(r-4.5-any)
ROntoTools_2.41.0.tar.gz(r-4.7-any)ROntoTools_2.41.0.tar.gz(r-4.6-any)
ROntoTools_2.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ROntoTools/json (API)

# Install 'ROntoTools' in R:

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

On BioConductor:ROntoTools-2.41.0(bioc 3.24)ROntoTools-2.40.0(bioc 3.23)

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

networkanalysis microarray graphsandnetworks

5.23 score 2 packages 20 scripts 7 mentions 15 exports 25 dependencies

Last updated from:421794b9f2. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	150
linux-devel-x86_64	WARNING	258
source / vignettes	OK	187
linux-release-x86_64	WARNING	273
macos-release-arm64	WARNING	141
macos-oldrel-arm64	WARNING	124
windows-devel	WARNING	167
windows-release	WARNING	163
windows-oldrel	WARNING	166
wasm-release	OK	101

Exports:alpha1MR alphaMLG compute.fisher compute.normalInv keggPathwayGraphs keggPathwayNames nodeWeights pDis pe peEdgeRenderInfo peNodeRenderInfo plot setEdgeWeights setNodeWeights Summary

Dependencies:askpass BiocGenerics Biostrings bitops boot crayon curl generics graph httr IRanges jsonlite KEGGgraph KEGGREST mime openssl png R6 RCurl Rgraphviz S4Vectors Seqinfo sys XML XVector

ROntoTools

Pathway-Express | Primary dis-regulation

Rendered fromrontotools.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute alpha weights	alpha1MR
Compute alpha weights	alphaMLG
Combine independent p-values using the Fisher method	compute.fisher
Combine independent p-values using the normal inversion method	compute.normalInv
Download and parse KEGG pathway data	keggPathwayGraphs
Obtain KEGG pathway titles	keggPathwayNames
Retrieve the node weights of a graph	nodeWeights 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 genes	pDis
Class that encodes the result of pDis analysis for a single pathway	pDisPathway-class
Primary dis-regulation (pDis) result class	pDisRes-class
Pathway-Express: Pathway analysis of signaling pathways	pe
Extract edge render information from a 'pePathway-class' object	peEdgeRenderInfo
Extract node render information from a 'pePathway-class' object	peNodeRenderInfo
Class that encodes the result of Pathway-Express for a single pathway	pePathway-class
Pathway-Express result class	peRes-class
Plot pathway level statistics	plot,pePathway,character-method plot,pePathway,missing-method
Plot Pathway-Express result	plot,peRes,character-method plot,peRes,missing-method
Set gene weights based on edge type	setEdgeWeights
Set node weights	setNodeWeights
Summarize the results of a Pathway-Express analysis	Summary,pDisRes-method
Summarize the results of a Pathway-Express analysis	Summary,peRes-method
Summarize the results of a primary dis-regulation (pDis) analysis	summary.pDisRes
Summarize the results of a Pathway-Express analysis	summary.peRes