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    25 repositories

    • anvio

      Public
      An analysis and visualization platform for 'omics data
      visualizationjavascriptpython
      visualizationjavascriptpythonsciencebioinformaticsmetagenomicscomparative-genomicspopulation-geneticsphylogenomicsmetatranscriptomics
      Python
      •
      GNU General Public License v3.0
      •158•513•176•10•Updated Apr 25, 2026Apr 25, 2026

    • anvio.org

      Public
      The anvi'o community web page
      HTML
      •14•6•3•1•Updated Apr 22, 2026Apr 22, 2026

    • merenlab.org

      Public
      Web content for Meren Lab
      HTML
      •
      MIT License
      •31•11•2•2•Updated Apr 16, 2026Apr 16, 2026

    • data-availability-checklist

      Public
      A data-conscious checklist for the reviewers of 'omics studies who champion open science
      Creative Commons Zero v1.0 Universal
      •0•5•0•0•Updated Apr 15, 2026Apr 15, 2026

    • hifmb-displays

      Public
      A tiny codebase to deal with the displays at the HIFMB foyer
      HTML
      •0•0•0•0•Updated Mar 29, 2026Mar 29, 2026

    • world-map-r

      Public
      A simple script to display stuff on a world map with R and ggplot
      R
      •
      GNU General Public License v3.0
      •4•17•1•0•Updated Feb 17, 2026Feb 17, 2026

    • clusterize

      Public
      The most basic SLURM wrapper
      Python
      •
      MIT License
      •2•1•0•0•Updated Feb 12, 2026Feb 12, 2026

    • rosalind

      Public
      A simple Meren Lab bot to notify our Slack regarding our jobs on the HPC System ROSA at UOL
      Python
      •0•0•0•0•Updated Dec 21, 2025Dec 21, 2025

    • illumina-utils

      Public
      A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
      Python
      •
      GNU General Public License v2.0
      •31•95•7•0•Updated Nov 24, 2025Nov 24, 2025

    • scholarly-report

      Public
      A few tools to generate reports for a bunch of scientists using their Google Scholar profiles.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 12, 2025Oct 12, 2025

    • reads-for-assembly

      Public
      Simulate metagenomic short reads from one or more populations.
      simulationmetagenomicsfasta
      simulationmetagenomicsfastafastqcontigs
      Python
      •
      GNU General Public License v2.0
      •4•26•0•0•Updated Jan 29, 2025Jan 29, 2025

    • public-marine-omics-metadata

      Public
      Semi-curated metadata for marine metagenomes (and other 'omics data types)
      R
      •0•1•4•0•Updated Sep 18, 2024Sep 18, 2024

    • oligotyping

      Public
      Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa
      Python
      •
      GNU General Public License v2.0
      •18•41•5•0•Updated Jun 24, 2024Jun 24, 2024

    • anviserver

      Public
      The code behind anvi'server
      HTML
      •
      GNU Affero General Public License v3.0
      •2•5•3•0•Updated May 9, 2023May 9, 2023

    • CONCOCT

      Public
      Clustering cONtigs with COverage and ComposiTion
      Python
      •
      Other
      •47•0•0•0•Updated Mar 22, 2022Mar 22, 2022

    • google-scholar-parser

      Public
      A set of Python utilities to parse Google Scholar data
      Python
      •
      GNU General Public License v3.0
      •0•4•5•0•Updated Jan 11, 2022Jan 11, 2022

    • SAAV-structural-mapping

      Public
      Map single amino acid variants onto protein structures. Modus operandi: explore relationships between genetic variation and structural biology.
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Oct 12, 2021Oct 12, 2021

    • mentorship-survey-workflow

      Public
      Python
      •1•1•0•0•Updated Jun 3, 2021Jun 3, 2021

    • tRNA-seq-tools

      Public
      Python
      •
      GNU General Public License v3.0
      •5•11•3•0•Updated Aug 6, 2019Aug 6, 2019

    • homebrew-anvio

      Public
      0•1•1•0•Updated Feb 18, 2019Feb 18, 2019

    • barhal-bot

      Public
      Our little Slack Bot that helps us keep an eye on our server
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 10, 2018Dec 10, 2018

    • BSD-QBio4

      Public
      Fourth BSD Quantitative Biology Bootcamp @ MBL
      R
      •
      GNU General Public License v3.0
      •9•0•0•0•Updated Aug 3, 2018Aug 3, 2018

    • BSD-QBio3

      Public
      BSD Bootcamp on Quantitative Biology 3
      HTML
      •
      GNU General Public License v3.0
      •8•0•0•0•Updated Jul 31, 2018Jul 31, 2018

    • MerenLab-workflows

      Public
      A repository with scripts to run pipeline that are commonly used in the Meren Lab
      Shell
      •
      GNU General Public License v3.0
      •4•11•8•0•Updated Feb 7, 2018Feb 7, 2018

    • gff_parser

      Public
      Parser to add external gene calls and functional annotation from Prokka to Anvi'o.
      Python
      •6•0•0•0•Updated May 18, 2017May 18, 2017
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