Repositories list

• anvio.org

  Public
  The anvi'o community web page

  HTML

  •12•6•2•1•Updated Oct 14, 2025Oct 14, 2025

• anvio

  Public
  An analysis and visualization platform for 'omics data

  visualizationjavascriptpython+ 9sciencebioinformaticsmetagenomicscomparative-genomicspopulation-geneticsphylogenomicsmetatranscriptomics+ 2

  Python

  •

  GNU General Public License v3.0

  •149•488•177•7•Updated Oct 14, 2025Oct 14, 2025

• merenlab.org

  Public
  Web content for Meren Lab

  HTML

  •

  MIT License

  •31•11•2•0•Updated Oct 12, 2025Oct 12, 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

• clusterize

  Public
  The most basic SLURM wrapper

  Python

  •

  MIT License

  •2•0•0•0•Updated Sep 17, 2025Sep 17, 2025

• 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 Apr 18, 2025Apr 18, 2025

• reads-for-assembly

  Public
  Simulate metagenomic short reads from one or more populations.

  simulationmetagenomicsfasta+ 2fastqcontigs

  Python

  •

  GNU General Public License v2.0

  •4•25•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

  •22•40•5•0•Updated Jun 24, 2024Jun 24, 2024

• 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

  •29•92•7•1•Updated Dec 16, 2023Dec 16, 2023

• 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 Sep 15, 2023Sep 15, 2023

• 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•3•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