A package to map transcriptome data to constrain reactions of a genome scale metabolic model
Project description
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map_transcriptome_data function
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Author: Soukaina Timouma E-mail: soukaina.timouma@gmail.com
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
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