To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MIGSA")

In most cases, you don't need to download the package archive at all.

MIGSA

DOI: 10.18129/B9.bioc.MIGSA    

Massive and Integrative Gene Set Analysis

Bioconductor version: Release (3.5)

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 mGSZrespectively. 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 bdmg.com.ar>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MIGSA")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MIGSA")

 

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

Details

biocViews GeneExpression, GeneSetEnrichment, KEGG, Microarray, RNASeq, Software, Visualization
Version 1.0.1
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL (>= 2)
Depends R (>= 3.4), methods, BiocGenerics
Imports AnnotationDbi, Biobase, BiocParallel, data.table, edgeR, futile.logger, ggplot2, GO.db, GOstats, gplots, graph, graphics, grDevices, GSEABase, limma, matrixStats, mGSZ, org.Hs.eg.db, RBGL, Rgraphviz, RJSONIO, stats, vegan
LinkingTo
Suggests breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, pbcmc, MIGSAdata
SystemRequirements
Enhances
URL http://www.bdmg.com.ar/
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source MIGSA_1.0.1.tar.gz
Windows Binary MIGSA_1.0.1.zip
Mac OS X 10.11 (El Capitan) MIGSA_1.0.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MIGSA
Package Short Url http://bioconductor.org/packages/MIGSA/
Package Downloads Report Download Stats

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