riptide

Release 3.4.81

Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe)

Homepage PyPI Python

Keywords
cobrapy, flux-sampling, flux-variability, metabolism, opencobra, pfba, transcriptomics
License
MIT
Install
pip install riptide==3.4.81

Documentation

=======
RIPTiDe
=======
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)

Stats

Dependencies
0
Dependent packages
0
Dependent repositories
0
Total releases
244
Latest release
First release
Stars
10
Forks
3
Watchers
3
Contributors
1
Repository size
4.53 MB
SourceRank
9

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Releases

3.4.81
3.4.80
3.4.79
3.4.78
3.4.77
3.4.76
3.4.75
3.4.74
3.4.73
3.4.72
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Contributors

Matt Jenior


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