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metaboGSE (version 1.2.3)

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

Description

Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) ).

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Version

Install

install.packages('metaboGSE')

Monthly Downloads

28

Version

1.2.3

License

GPL-3

Maintainer

Van T. Tran

Last Published

January 7th, 2020

Functions in metaboGSE (1.2.3)

Description of gene set IDs

simulateSubmnet

Plot fitness of submodels built by gene removal in a condition

Gene set enrichment analysis

Compute weights of rescue reactions

GO annotation retrieved from Uniprot

parseBooleanCopy

Copy of sybil:::.parseBoolean

Identify the best ranking

Structure of Class "scoreGeneDel"

Generate a submodel by removing genes

Simulation of gene removal-based submodel series with a given ranking

Compute distances of rescue reactions

Relative expression data (log2 counts)

Submodel construction example for Yarrowia lipolytica

Gene set enrichment example for Yarrowia lipolytica

Z-score of expression data

Compute maxium area between curves

Relax model external source

iMK735 metabolic models in hypoxia and normoxia

A fixed version of sybil::addReact

Fitness of gene removal-based submodels with different gene rankings

Abbreviate GO term description

Compute area between two curves

diagnosticTolerance

Compute appropriate tolerance for the given model

Gene expression from Maguire et al. RNA-seq data