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
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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")
| R Script | Getting pbcmc datasets | |
| R Script | Getting TCGA datasets | |
| R Script | Massive and Integrative Gene Set Analysis | |
| 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) (0.5 years) |
| 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.
| Source Package | 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 |
Documentation »
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