qpgraph

DOI: 10.18129/B9.bioc.qpgraph    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see qpgraph.

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Bioconductor version: 3.10

Estimate gene and eQTL networks from high-throughput expression and genotyping assays.

Author: Robert Castelo [aut, cre], Alberto Roverato [aut]

Maintainer: Robert Castelo <robert.castelo at upf.edu>

Citation (from within R, enter citation("qpgraph")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("qpgraph")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("qpgraph")

 

PDF BasicUsersGuide.pdf
PDF R Script Estimate eQTL networks using qpgraph
PDF R Script Reverse-engineer transcriptional regulatory networks using qpgraph
PDF R Script Simulating molecular regulatory networks using qpgraph
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, GeneRegulation, GeneticVariability, Genetics, GraphAndNetwork, Microarray, NetworkInference, Pathways, SNP, Software, Transcription
Version 2.20.0
In Bioconductor since BioC 2.4 (R-2.9) (11 years)
License GPL (>= 2)
Depends R (>= 3.4)
Imports methods, parallel, Matrix (>= 1.0), grid, annotate, graph(>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz
LinkingTo
Suggests RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats
SystemRequirements
Enhances
URL https://github.com/rcastelo/qpgraph
BugReports https://github.com/rcastelo/rcastelo/issues
Depends On Me
Imports Me clipper
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package qpgraph_2.20.0.tar.gz
Windows Binary qpgraph_2.20.0.zip
Mac OS X 10.11 (El Capitan) qpgraph_2.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/qpgraph
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/qpgraph
Package Short Url https://bioconductor.org/packages/qpgraph/
Package Downloads Report Download Stats

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