qpgraph

DOI: 10.18129/B9.bioc.qpgraph    

This package is for version 3.9 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: 3.9

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>

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	2.18.0
In Bioconductor since	BioC 2.4 (R-2.9) (10.5 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_2.18.0.tar.gz
Windows Binary	qpgraph_2.18.0.zip
Mac OS X 10.11 (El Capitan)	qpgraph_2.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/qpgraph
Source Repository (Developer Access)	git clone [email protected]:packages/qpgraph
Package Short Url	https://bioconductor.org/packages/qpgraph/
Package Downloads Report	Download Stats