Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
☆10Jun 25, 2024Updated last year
Alternatives and similar repositories for scfa_predictions
Users that are interested in scfa_predictions are comparing it to the libraries listed below
Sorting:
- MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome☆16Nov 7, 2019Updated 6 years ago
- the Metagenomic test for Presence Or Absence of Pathways☆13Mar 4, 2019Updated 7 years ago
- Open prediction of Polysaccharide Utilisation Loci (PUL)☆25Apr 22, 2020Updated 5 years ago
- ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test☆15Mar 7, 2019Updated 7 years ago
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆257Jul 27, 2024Updated last year
- A manually curated database of human gut metabolic modules.☆17Jul 27, 2018Updated 7 years ago
- iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline☆13Feb 10, 2026Updated last month
- A healthy human gut genome collection☆25Aug 21, 2025Updated 7 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆27Jul 22, 2024Updated last year
- METAgenomic LONgitudinal Differential Abundance method☆16Dec 17, 2019Updated 6 years ago
- BiomeNED main code☆12Jul 25, 2019Updated 6 years ago
- hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis☆70Feb 9, 2025Updated last year
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆24Jan 24, 2024Updated 2 years ago
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆11Oct 11, 2022Updated 3 years ago
- Guide to processing raw LCMS metabolomic and lipidomic data using MS-DIAL, followed by data pre-processing and secondary annotation (of m…☆24Feb 5, 2024Updated 2 years ago
- Produce scientific figures in R that look exactly how you want☆18Jan 17, 2026Updated 2 months ago
- Snakemake workflow to detect and classify viruses in metagenome assemblies.☆19Feb 14, 2024Updated 2 years ago
- gutSMASH☆58Oct 3, 2025Updated 5 months ago
- Sample Metadata Curation for curatedMetagenomicData☆30Updated this week
- Kraken(2) database based on the GTDB project☆28Dec 20, 2018Updated 7 years ago
- ☆10Dec 29, 2021Updated 4 years ago
- Python package to study microbial communities using metabolic modeling.☆121Mar 11, 2026Updated last week
- Pipeline for metagenome and metatranscriptome joint assembly☆20Mar 3, 2023Updated 3 years ago
- annotating microbial co-occurrence networks☆12Oct 7, 2025Updated 5 months ago
- CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification …☆12Mar 20, 2022Updated 4 years ago
- ☆18Dec 11, 2024Updated last year
- Cytoscape interface to STRING and STITCH☆11May 9, 2025Updated 10 months ago
- MetaCompass: Reference-guided Assembly of Metagenomes☆43Aug 13, 2025Updated 7 months ago
- MGnify RESTful API☆10Feb 11, 2026Updated last month
- ☆10Dec 15, 2023Updated 2 years ago
- Alignment-free Phylogenetic Placement using filtered SPAced word Matches☆12Jul 19, 2023Updated 2 years ago
- Dynamic FBA for use with COBRApy metabolic models☆10Sep 26, 2023Updated 2 years ago
- A command-line tool for profiling CAZyme abundances in metagenomic datasets.☆16Updated this week
- ☆40Dec 16, 2023Updated 2 years ago
- Functions for compositional analysis of high throughput sequencing☆29Dec 8, 2023Updated 2 years ago
- DNAscan2 is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring v…☆14May 7, 2024Updated last year
- A set of programs for the taxonomic analysis of genetic sequences☆14Jun 12, 2023Updated 2 years ago
- A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.☆23Aug 14, 2025Updated 7 months ago
- ☆43Nov 20, 2017Updated 8 years ago