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 (!require("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")
BasicUsersGuide.pdf PDF
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 R Script
Reference Manual PDF
NEWS Text

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) (15 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
System Requirements
URL https://github.com/rcastelo/qpgraph
Bug Reports https://github.com/rcastelo/rcastelo/issues
See More
Suggests RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats
Linking To
Enhances
Depends On Me
Imports Me clipper
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/qpgraph/
Package Short Url https://bioconductor.org/packages/qpgraph/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive