rcolpo / pgp_reconstruction
Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
☆12Updated last year
Alternatives and similar repositories for pgp_reconstruction:
Users that are interested in pgp_reconstruction are comparing it to the libraries listed below
- ☆38Updated 3 months ago
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆11Updated 2 years ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆13Updated last year
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆25Updated 6 years ago
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆17Updated 2 years ago
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆19Updated last week
- Pipeline for major biological analyses.☆34Updated 2 years ago
- lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters☆37Updated 7 months ago
- A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data☆78Updated 4 months ago
- CLI tool to annotate genes with KOfam☆77Updated last year
- Metaphor: a general-purpose workflow for assembly and binning of metagenomes☆39Updated 4 months ago
- Pipelines used in the lab.☆12Updated 5 months ago
- A tool for representing genomic potential and transcriptomic expression into KEGG pathways☆54Updated 7 months ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆58Updated 3 weeks ago
- Bioinformatic Tools for study Evolution of metabolic diversity☆31Updated last year
- SMETANA: a tool to analyse interactions in microbial communities☆58Updated 4 years ago
- From annotated genomes to metabolic screening in large scale microbiotas☆56Updated 2 weeks ago
- A package to annotate protein sequences☆55Updated last month
- Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.☆67Updated 2 months ago
- Open-source bioinformatics pipeline for the preprocessing of raw amplicon sequencing / metabarcoding data.☆12Updated 2 months ago
- BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor☆14Updated last year
- Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)☆41Updated 3 months ago
- Python package to study microbial communities using metabolic modeling.☆98Updated 3 weeks ago
- The Microbial Co-occurrence Network Explorer☆20Updated last year
- MacSyFinder models allowing for a systematic search of anti-phage systems☆22Updated last month
- Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset☆20Updated 4 years ago
- ☆43Updated last month
- A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes☆34Updated last year
- ☆29Updated this week
- ☆11Updated 5 years ago