MIGSA
This package is for version 3.16 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: 3.16
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("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 | R Script | |
| Getting TCGA datasets | R Script | |
| Massive and Integrative Gene Set Analysis | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, KEGG, Microarray, RNASeq, Software, Visualization |
| Version | 1.21.0 |
| 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_1.21.0.tar.gz |
| Windows Binary | MIGSA_1.21.0.zip |
| macOS Binary (x86_64) | MIGSA_1.21.0.tgz |
| 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 |
| 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 3.16 | Source Archive |