qLSLab / GPRuler
GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabolic networks of a given organism based on the corresponding list of genes involved in catalysis of each metabolic reaction, and genes-to-reaction associations.
☆11Updated 2 years ago
Alternatives and similar repositories for GPRuler:
Users that are interested in GPRuler are comparing it to the libraries listed below
- Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models☆12Updated last year
- Supplementary data for co-occurrence manuscript☆10Updated 5 years ago
- ☆38Updated 3 months ago
- ☆11Updated 5 years ago
- Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)☆41Updated 3 months ago
- Pipeline for major biological analyses.☆34Updated 3 years ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆17Updated 7 months ago
- BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor☆14Updated last year
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆17Updated 2 years ago
- KEGG Module Evaluation Tool☆29Updated last year
- SMBGC Annotation using Neural Networks Trained on Interpro Signatures☆26Updated last month
- Rapid discovery of novel prophages using biological feature engineering and machine learning☆37Updated 3 months ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆13Updated last year
- The Microbial Co-occurrence Network Explorer☆20Updated last year
- scripts for predicting natural product activity from biosynthetic gene cluster sequences☆23Updated 2 years ago
- lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters☆37Updated last week
- ☆12Updated 3 years ago
- BiG-MEx implementation as Docker images and R packages☆13Updated 3 years ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆39Updated 3 weeks ago
- Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data☆16Updated this week
- Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut☆10Updated 9 months ago
- A package to annotate protein sequences☆56Updated last month
- A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.☆17Updated 5 months ago
- Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species☆12Updated 4 years ago
- ☆45Updated last year
- ☆19Updated 3 years ago
- Pipelines used in the lab.☆12Updated last week
- GCN classifier for phage taxanomy classification☆31Updated 4 months ago
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆19Updated last week
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins☆13Updated 3 years ago