Repositories list

• Bio334

  Public
  Bio334 Public student repository

  Jupyter Notebook

  •10•4•0•0•Updated Feb 24, 2026Feb 24, 2026

• MicrobeAtlas_companion

  Public
  Code and additional supplementary data for Rodrigues, Tackmann et al. (2025)

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jan 20, 2026Jan 20, 2026

• string-mcp

  Public
  STRING MCP server

  Python

  •

  MIT License

  •2•5•0•0•Updated Dec 11, 2025Dec 11, 2025

• paxdb-issues

  Public
  🧩 PaxDb Issues Welcome to the PaxDb Issue Tracker — the central place to report, discuss, and track issues related to PaxDb, the Protein Abundance Database.

  0•0•1•0•Updated Nov 10, 2025Nov 10, 2025

• FlashWeave.jl

  Public
  Inference of microbial interaction networks from large-scale heterogeneous abundance data

  metadatabioinformaticsjulia+ 7

  metadatabioinformaticsjuliametagenomicshigh-performance-computingmicrobiomeprobabilistic-graphical-modelsco-occurencecompositional-dataecological-network

  Julia

  •

  Other

  •9•90•10•0•Updated Oct 9, 2025Oct 9, 2025

• paxdb-data-pipeline

  Public

  meringlab/paxdb-data-pipeline’s past year of commit activity
  proteinsabundance

  proteinsabundance

  Python

  •0•0•4•0•Updated Jul 26, 2024Jul 26, 2024

• MAPseq

  Public
  highthroughput rRNA sequence classification and OTU mapping for metagenomic samples

  C

  •

  Other

  •8•0•0•0•Updated Jun 7, 2024Jun 7, 2024

• MAPseq_clone

  Public
  C

  •

  Other

  •0•0•0•0•Updated May 2, 2024May 2, 2024

• react-map-web

  Public
  JavaScript

  •0•0•0•0•Updated Aug 3, 2023Aug 3, 2023

• paxdb-api

  Public
  abundance microservice

  JavaScript

  •

  Other

  •0•0•1•15•Updated Jul 18, 2023Jul 18, 2023

• paxdb-orthology-api

  Public
  orthology api frontend

  JavaScript

  •

  Other

  •0•0•0•0•Updated Feb 10, 2023Feb 10, 2023

• paxdb-search

  Public
  search microservice

  Java

  •0•0•1•0•Updated Feb 9, 2023Feb 9, 2023

• paxdb-orthology-lib

  Public
  pax-db.org orthology API npm module

  JavaScript

  •

  Other

  •0•0•4•5•Updated Feb 9, 2023Feb 9, 2023

• MicrobeAtlasWebsite

  Public
  0•8•5•0•Updated Dec 17, 2022Dec 17, 2022

• annotation_system_assessment

  Public
  Snakemake pipeline to benchmark 11 functional pathway annotation systems

  genomicstranscriptomicspathway-analysis+ 2

  genomicstranscriptomicspathway-analysisfunctional-annotationgene-set-enrichment-analysis

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 30, 2022Jun 30, 2022

• og_consistency_pipeline

  Public
  Consistency pipeline for hierarchies of orthologous groups (OGs) based on subsampling and tree reconciliation

  Python

  •

  GNU General Public License v3.0

  •3•5•0•0•Updated Nov 22, 2018Nov 22, 2018

• paxdb-orthology

  Public
  DEPRECATED use lib&storage&api repos

  JavaScript

  •

  Other

  •0•0•3•0•Updated Aug 9, 2018Aug 9, 2018

• gene-assassin-app-score

  Public
  geneassassin.com application scoring

  Python

  •0•0•1•0•Updated Mar 20, 2018Mar 20, 2018

• gene_assassin_api

  Public
  geneassassin.org API (guides, proteins, primers, ...)

  0•0•0•0•Updated Feb 7, 2018Feb 7, 2018

• mltreemap

  Public
  accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

  HTML

  •

  MIT License

  •0•0•0•0•Updated Aug 17, 2017Aug 17, 2017

• stringdb-psicquic

  Public
  The official http://string-db.org PSICQUIC implementation.

  Java

  •

  Apache License 2.0

  •0•1•0•0•Updated May 29, 2017May 29, 2017

• cellbase-docker

  Public
  dockerised opencb/cellbase

  Perl

  •

  Apache License 2.0

  •1•2•0•0•Updated Jan 25, 2017Jan 25, 2017

• MAPseq-HMP_reanalysis

  Public
  This repository contains code used to reanalyse Human Microbiome Project data to benchmark MAPseq.

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 19, 2016Oct 19, 2016

• stringdb-jdbc

  Public
  Java utilities for http://string-db.org PostgreSQL data

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 27, 2016Jan 27, 2016