qpgraph

This is the development version of qpgraph; for the stable release version, see qpgraph.

Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data

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DOI: 10.18129/B9.bioc.qpgraph

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GeneRegulation, GeneticVariability, Genetics, GraphAndNetwork, Microarray, NetworkInference, Pathways, SNP, Software, Transcription

Version 2.45.0

In Bioconductor since BioC 2.4 (R-2.9) (16.5 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, Seqinfo, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz

System Requirements

URL https://github.com/rcastelo/qpgraph

Bug Reports https://github.com/rcastelo/qpgraph/issues

Suggests RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats

Linking To

Enhances

Depends On Me

Imports Me clipper, MOSClip, topologyGSA

Suggests Me

Links To Me

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Package Archives

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

Source Package qpgraph_2.45.0.tar.gz

Windows Binary (x86_64) qpgraph_2.45.0.zip (64-bit only)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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