Repositories list

• KADAIF

  Public
  An anomaly detection method specifically designed for microbiome data.

  Jupyter Notebook

  •0•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• microbiome_metabolic_adaptation

  Public
  R

  •0•0•0•0•Updated Feb 13, 2025Feb 13, 2025

• mimosa2

  Public
  R

  •

  GNU General Public License v3.0

  •6•13•4•0•Updated Dec 16, 2024Dec 16, 2024

• microbiome-metabolome-curated-data

  Public
  HTML

  •

  MIT License

  •27•62•1•0•Updated Oct 16, 2024Oct 16, 2024

• multi_view_integration_analysis

  Public
  R

  •0•11•0•0•Updated Jun 6, 2024Jun 6, 2024

• RDR

  Public
  R

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated May 5, 2024May 5, 2024

• longitudinal_interpolation

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Apr 18, 2024Apr 18, 2024

• IIRN_multi_omic

  Public
  Multiomic analysis for the paper titled "Integrative analysis of untargeted serum and fecal metabolome and gut microbiome reveals a role in Crohn Disease and with signals that precede a disease flare"

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 17, 2024Jan 17, 2024

• vaginal_microbiome_manifold

  Public
  Manifold detection

  Jupyter Notebook

  •0•0•0•0•Updated Dec 28, 2023Dec 28, 2023

• MIMOSA2shiny

  Public
  R

  •

  GNU General Public License v3.0

  •0•2•1•0•Updated Dec 19, 2023Dec 19, 2023

• SOURCE_multiomics

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 15, 2023Jun 15, 2023

• drug_microbiome

  Public
  Data and code for paper "A data-driven approach for predicting the impact of drugs on the human microbiome"

  R

  •

  GNU General Public License v3.0

  •0•8•0•0•Updated Apr 20, 2023Apr 20, 2023

• IFDP

  Public
  Python

  •1•1•0•0•Updated Dec 13, 2022Dec 13, 2022

• microbiome_temporal_alignment

  Public
  Jupyter Notebook

  •0•1•0•0•Updated May 13, 2022May 13, 2022

• burrito

  Public
  A visualization tool for exploratory data analysis of metagenomic data

  JavaScript

  •

  GNU General Public License v3.0

  •9•37•20•0•Updated Mar 22, 2022Mar 22, 2022

• robustness

  Public
  R

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Feb 11, 2022Feb 11, 2022

• robustness_of_gut_microbiome-metabolite_associations

  Public
  R

  •3•2•0•0•Updated Dec 14, 2021Dec 14, 2021

• MetaLAFFA

  Public
  A bioinformatics pipeline for annotating functional capacities in shotgun metagenomic data with native compute cluster integration

  Python

  •

  GNU General Public License v3.0

  •3•7•6•0•Updated Nov 16, 2021Nov 16, 2021

• fishtaco

  Public
  FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts

  Python

  •

  Other

  •4•24•10•0•Updated Jul 3, 2021Jul 3, 2021

• fishtaco-plot

  Public
  R

  •0•3•0•0•Updated Jul 3, 2021Jul 3, 2021

• MIMOSA

  Public
  Model-based Integration of Metabolite Observations and Species Abundances

  R

  •9•24•0•0•Updated Feb 21, 2020Feb 21, 2020

• T6SS

  Public
  Python

  •0•0•0•0•Updated Jan 14, 2020Jan 14, 2020

• MUSiCC

  Public
  MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5•16•6•0•Updated Nov 7, 2019Nov 7, 2019

• microbiome-metabolome-evaluation

  Public
  R

  •0•3•0•0•Updated Sep 3, 2019Sep 3, 2019

• CoMiDA

  Public
  The code and distributable for designing minimal microbial communities with specified metabolic functions.

  C++

  •

  Other

  •3•11•0•0•Updated Aug 9, 2017Aug 9, 2017

• empanada

  Public
  empanada is a tool for evidence-based assignment of genes to pathways in metagenomic data

  Python

  •

  Other

  •2•3•1•0•Updated Feb 13, 2016Feb 13, 2016