Metadata-Version: 1.0
Name: riptide
Version: 1.7
Summary: Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe)
Home-page: https://github.com/mjenior/riptide
Author: Matt Jenior
Author-email: mattjenior@gmail.com
License: MIT
Description: RIPTiDe
        =======
        
        Reaction Inclusion by Parsimonious usage and Transcript Distribution
        
        Transcriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment. While traditional analyses have been informative, leveraging these datasets within genome-scale metabolic network reconstructions (GENREs) can provide greatly improved context for shifts in pathway utilization and downstream/upstream ramifications for changes in metabolic regulation. Previous techniques for GENRE transcript integration have focused on creating maximum consensus with the input datasets. However, these approaches have collectively performed poorly for metabolic predictions even compared to transcript-agnostic approaches of flux minimization (pFBA) that identifies the most efficient patterns of metabolism given certain growth constraints. Our new method, RIPTiDe, combines these concepts and utilizes overall minimization of flux in conjunction with transcriptomic analysis to identify the most energy efficient pathways to achieve growth that include more highly transcribed enzymes. RIPTiDe requires a low level of manual intervention which leads to reduced bias in predictions. 
        
        
        Please cite when using::
        
            Jenior ML, Moutinho TJ, and Papin JA. (2019). Parsimonious transcript data integration improves context-specific predictions of bacterial metabolism in complex environments. BioRxiv.
        
        
        Installation
        ------------
        
        Installation is simply::
        
            pip install riptide
        
        .. 
        
        Other dependencies include both cobrapy and symengine which are automatically installed. 
        Cobrapy should be >=version 0.13
        
        .. _riptide: https://github.com/mjenior/riptide
        
        
        
        Example Use
        -----------
        
        Be sure to check out the `Example Notebook`_ that demos ``omfvista``!
        Here's an example using the sample data hosted in the `OMF repository`_.
        
        
        .. code-block:: python
        
            from riptide import *
        
            my_model = cobra.io.read_sbml_model('examples/genre.sbml')
        
            transcript_abundances_1 = read_transcription_file('examples/transcriptome1.tsv')
            transcript_abundances_2 = read_transcription_file('examples/transcriptome2.tsv')
        
            riptide_object_1 = riptide(my_model, transcript_abundances_1)
            riptide_object_2 = riptide(my_model, transcript_abundances_2)
        .. 
        
        The resulting RIPTiDe object properties::
        
            model = contextualized genome-scale metabolic network reconstruction
            fluxes = Flux sampling or flux variability analysis pandas object
            quantile_range = percentile intervals by which to parse transcript abundance distribution
            linear_coefficient_range = linear coeeficients assigned to corresponding quantile
            fraction_of_optimum = minimum percentage of optimal allowable flux through the objective during contextualization
        
        .. 
        
        Thank you for your interest in RIPTiDe, for additional questions please email mljenior@virginia.edu.
        
        
Platform: UNKNOWN
