GSMM-transcriptome-data-mapper 0.0.1

A package to map transcriptome data to constrain reactions of a genome scale metabolic model

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map_transcriptome_data function

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Author: Soukaina Timouma E-mail: [e-mail]

The purpose of this function is to enable the mapping of transcriptome data into a genome scale metabolic model reactions, enabling the imposition of restrictions that accurately represent the experimental conditions being investigated.

map_transcriptome_data() required 4 positional arguments: 'model', 'transcriptomeData', 'threshold_abundance', and 'max_bound'

• 'model': genome scale model
• 'transcriptomeData': dictionary containing the gene IDs (as written in the genome scale model) as keys and the transcription levels as values.
• 'threshold_abundance': threshold to consider that a gene is expressed rather than be noise. For example you can set the threshold to 10 as recommended in DESeq2 documentation.
• 'max_bound': the value of the upper bounds when there is no restriction. For example, in Yeast8 model, the lower and upper bounds range from -1000 to 1000. For Yeast8 model, the 'max_bound' is 1000.

Installation:

python3 -m pip install GSMM_transcriptome_data_mapper