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


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Documentation for package ‘metaboGSE’ version 1.2.1

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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