# Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data

## Documentation for package ‘metaboGSE’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

bestRanking | Identify the best ranking
exprMaguire | Gene expression from Maguire et al. RNA-seq data
fitness | Fitness of gene removal-based submodels with different gene rankings
iMK735 | iMK735 metabolic models in hypoxia and normoxia
metaboGSE | Gene set enrichment analysis
pwDesc | Description of gene set IDs
relativeExpr | Relative expression data (log2 counts)
rescue | Rescue a model
rmGenes | Generate a submodel by removing genes
scoreGeneDel | Structure of Class "scoreGeneDel"
simulateSubmnet | Plot fitness of submodels built by gene removal in a condition
submnet | Simulation of gene removal-based submodel series with a given ranking
weightReacts | Compute weights of rescue reactions
yarli2GO | GO annotation retrieved from Uniprot
yarliGOdata | topGOdata object built from yarli2GO
yarliGSE | Gene set enrichment example for Yarrowia lipolytica
yarliSubmnets | Submodel construction example for Yarrowia lipolytica
zscoreExpr | Z-score of expression data