Reconstructing the Transcriptional Regulatory Network of Probiotic L. reuteri is Enabled by Transcriptomics and Machine Learning
Creators
- 1. The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
- 2. Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
Description
LactoPRECISE: A comprehensive framework exploring Lactobacillus reuteri's genetic diversity, regulatory networks, and functional annotations for personalized medicine and microbial therapeutics.
This repository presents a computational workflow to compute and characterize all iModulons for a selected organism. This occurs in five steps:
Gather all publicly available RNA-seq data for the organism (Step 1) Process the RNA-seq data (Step 2) Inspect data to identify high-quality datasets (Step 3) Compute iModulons (Step 4) Characterize iModulons using PyModulon (Step 5)
iModulons are independently-modulated groups of genes that are computed through Independent Component Analysis (ICA) of a gene expression dataset. To learn more about iModulons or explore published iModulons, visit iModulonDB or see our publications for Escherichia coli, Staphylococcus aureus, or Bacillus subtilis.
A pre-print is being prepared for this tutorial workflow.
Files
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