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qpgraph

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


Bioconductor version: Release (3.18)

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 "4.3") 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 2.36.0
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License GPL (>= 2)
Depends R (>= 3.5)
Imports methods, parallel, Matrix (>= 1.5-0), 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
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Package Archives

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

Source Package qpgraph_2.36.0.tar.gz
Windows Binary qpgraph_2.36.0.zip
macOS Binary (x86_64) qpgraph_2.36.0.tgz
macOS Binary (arm64) qpgraph_2.36.0.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