Learn R Programming

metaboGSE (version 1.2.5)

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) ).

Copy Link

Version

Install

install.packages('metaboGSE')

Monthly Downloads

21

Version

1.2.5

License

GPL-3

Maintainer

Van T. Tran

Last Published

October 22nd, 2020

Functions in metaboGSE (1.2.5)

GO annotation retrieved from Uniprot

Relative expression data (log2 counts)

iMK735 metabolic models in hypoxia and normoxia

Description of gene set IDs

Compute maxium area between curves

diagnosticTolerance

Compute appropriate tolerance for the given model

simulateSubmnet

Plot fitness of submodels built by gene removal in a condition

Gene expression from Maguire et al. RNA-seq data

Structure of Class "scoreGeneDel"

Generate a submodel by removing genes

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

Z-score of expression data

Gene set enrichment analysis

parseBooleanCopy

Copy of sybil:::.parseBoolean

Gene set enrichment example for Yarrowia lipolytica

Submodel construction example for Yarrowia lipolytica

Identify the best ranking

Compute area between two curves

Fitness of gene removal-based submodels with different gene rankings

Abbreviate GO term description

Relax model external source

A fixed version of sybil::addReact

Compute distances of rescue reactions

Compute weights of rescue reactions