MIGSA

DOI: 10.18129/B9.bioc.MIGSA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MIGSA.

Massive and Integrative Gene Set Analysis

Bioconductor version: 3.9

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 bdmg.com.ar>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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	1.8.1
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 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, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, RJSONIO, stats, utils, vegan
LinkingTo
Suggests	breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ, MIGSAdata
SystemRequirements
Enhances
URL	http://www.bdmg.com.ar/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MIGSA_1.8.1.tar.gz
Windows Binary	MIGSA_1.8.1.zip
Mac OS X 10.11 (El Capitan)	MIGSA_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MIGSA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MIGSA
Package Short Url	https://bioconductor.org/packages/MIGSA/
Package Downloads Report	Download Stats