Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut
☆10Jun 25, 2024Updated 2 years ago
Alternatives and similar repositories for scfa_predictions
Users that are interested in scfa_predictions are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆15Mar 15, 2026Updated 7 months ago
- Collection of genome-scale metabolic models, genomes, and scripts for At-LSPHERE bacterial culture collection☆10Jul 25, 2023Updated 3 years ago
- MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome☆18Nov 7, 2019Updated 6 years ago
- GEMsembler tool for assembling and comparing several types of Genome-Scale Metabolic Models (GEMs)☆14Jun 29, 2026Updated 4 months ago
- COnstraint Based Reconstruction and EXascale Analysis (in Julia)☆20Sep 26, 2025Updated last year
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- A healthy human gut genome collection☆26Aug 21, 2025Updated last year
- ☆19May 8, 2024Updated 2 years ago
- the Metagenomic test for Presence Or Absence of Pathways☆13Mar 4, 2019Updated 7 years ago
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆274May 13, 2026Updated 5 months ago
- Open prediction of Polysaccharide Utilisation Loci (PUL)☆27Apr 22, 2020Updated 6 years ago
- Snakemake pipeline for annotating metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆11Jul 11, 2018Updated 8 years ago
- ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test☆15Mar 7, 2019Updated 7 years ago
- ☆24Oct 19, 2023Updated 3 years ago
- Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake☆49Mar 6, 2024Updated 2 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Python package for building and analyzing models using ModelSEED☆31Feb 11, 2026Updated 8 months ago
- A manually curated database of human gut metabolic modules.☆19Updated this week
- Build a map of genes present across a set of microbial genomes☆18Jan 23, 2026Updated 9 months ago
- mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models☆15Aug 20, 2025Updated last year
- iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline☆13Feb 10, 2026Updated 8 months ago
- An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as…☆71Updated this week
- METAgenomic LONgitudinal Differential Abundance method☆15Dec 17, 2019Updated 6 years ago
- BiomeNED main code☆12Jul 25, 2019Updated 7 years ago
- Python interface for running COMETS simulations and analyzing the results☆15May 19, 2026Updated 5 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆26Jul 22, 2024Updated 2 years ago
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆24Jan 24, 2024Updated 2 years ago
- hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis☆71Feb 9, 2025Updated last year
- Enzyme-constrained genome-scale models in python☆39Oct 25, 2023Updated 3 years ago
- From annotated genomes to metabolic screening in large scale microbiotas☆77Oct 16, 2026Updated 2 weeks ago
- Produce scientific figures in R that look exactly how you want☆18Jan 17, 2026Updated 9 months ago
- Pipeline for metagenome and metatranscriptome joint assembly☆21Mar 3, 2023Updated 3 years ago
- Kraken(2) database based on the GTDB project☆28Dec 20, 2018Updated 7 years ago
- Code depository for papers☆27Sep 16, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Snakemake workflow to detect and classify viruses in metagenome assemblies.☆19Feb 14, 2024Updated 2 years ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Apr 1, 2023Updated 3 years ago
- gutSMASH☆60Oct 3, 2025Updated last year
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆38Apr 26, 2026Updated 6 months ago
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆89Oct 19, 2026Updated last week
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆13Oct 11, 2022Updated 4 years ago
- CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification …☆12Mar 20, 2022Updated 4 years ago