MIGSA

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MIGSA.

Massive and Integrative Gene Set Analysis


Bioconductor version: 3.15

Massive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and mGSZ respectively. The greatest strengths of this big omics data tool are the availability of several functions to explore, analyze and visualize its results in order to facilitate the data mining task over huge information sources. MIGSA package also provides several functions that allow to easily load the most updated gene sets from several repositories.

Author: Juan C. Rodriguez, Cristobal Fresno, Andrea S. Llera and Elmer A. Fernandez

Maintainer: Juan C. Rodriguez <jcrodriguez at unc.edu.ar>

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

Installation

To install this package, start R (version "4.2") and enter:


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

BiocManager::install("MIGSA")

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("MIGSA")
Getting pbcmc datasets PDF R Script
Getting TCGA datasets PDF R Script
Massive and Integrative Gene Set Analysis PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneSetEnrichment, KEGG, Microarray, RNASeq, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL (>= 2)
Depends R (>= 3.4), methods, BiocGenerics
Imports AnnotationDbi, Biobase, BiocParallel, compiler, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, jsonlite, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, stats, utils, vegan
System Requirements
URL https://github.com/jcrodriguez1989/MIGSA/
Bug Reports https://github.com/jcrodriguez1989/MIGSA/issues
See More
Suggests BiocStyle, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MIGSA_1.20.0.tar.gz
Windows Binary MIGSA_1.20.0.zip (64-bit only)
macOS Binary (x86_64) MIGSA_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MIGSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MIGSA
Bioc Package Browser https://code.bioconductor.org/browse/MIGSA/
Package Short Url https://bioconductor.org/packages/MIGSA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive