MIGSA

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Massive and Integrative Gene Set Analysis

Bioconductor version: Release (3.17)

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 "4.3") 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


Reference Manual	PDF

Details

biocViews	GeneExpression, GeneSetEnrichment, KEGG, Microarray, RNASeq, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 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, jsonlite, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, stats, utils, vegan
Linking To
Suggests	BiocStyle, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit
System Requirements
Enhances
URL	https://github.com/jcrodriguez1989/MIGSA/
Bug Reports	https://github.com/jcrodriguez1989/MIGSA/issues

Depends On Me
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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