Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe)
Project description
Reaction Inclusion by Parsimonious usage and Transcript Distribution
# Please cite when using: Jenior ML and Papin JA. (2018) RIPTiDe: Metabolic model contextualization through exploration of mutliple transcription and flux minimization levels. BioRxiv. DOI
# Dependencies cobrapy (>=version 0.14)
symengine
# Example usage: my_model = cobra.io.read_sbml_model(‘my_model.sbml’)
transcript_abundances = read_transcription_file(‘reads_to_genes.tsv’, replicates=True)
contextualized_model, flux_samples = riptide(my_model, transcript_abundances)
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