Metadata-Version: 2.1
Name: GSMM_transcriptome_data_mapper
Version: 0.0.1
Summary: A package to map transcriptome data to constrain reactions of a genome scale metabolic model
Project-URL: Homepage, https://github.com/Sookie-S/Mapping-of-transcriptome-data-to-genome-scale-scale-model-reactions
Project-URL: Bug Tracker, https://github.com/Sookie-S/Mapping-of-transcriptome-data-to-genome-scale-scale-model-reactions/issues
Author-email: Soukaina Timouma <soukaina.timouma@gmail.com>
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown

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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