Repositories list

• academic-kickstart

  Public
  Easily create a beautiful website using Academic and Hugo

  TeX

  •

  MIT License

  •6.5k6.5k forks•22 stars•00 issues•00 pull requests•Updated Mar 13, 2026Mar 13, 2026

• AlexanderLabWHOI.github.io

  Public
  Alexander Lab at Woods Hole Oceanographic Institution

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 13, 2026Mar 13, 2026

• eukrhythmic

  Public
  A metatranscriptomic pipeline optimized for the study of microeukaryotes.

  Python

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  MIT License

  •55 forks•1717 stars•1919 issues•33 pull requests•Updated Dec 30, 2025Dec 30, 2025

• 2025-06-26-PythonCarpentries

  Public
  HTML

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  Other

  •44 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2025Jun 18, 2025

• EUKulele

  Public
  Automatic eukaryotic taxonomic classification

  Python

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  MIT License

  •77 forks•2929 stars•2424 issues•00 pull requests•Updated May 9, 2025May 9, 2025

• Alexander_phylogeny_tutorial

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2025Apr 24, 2025

• ehux_annotation_consensus

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2025Mar 24, 2025

• 2024-Krinos-Ghux-Darwin

  Public
  Code for Krinos et al. G. huxleyi vital rates paper with Darwin model analysis

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 20, 2024Nov 20, 2024

• 2023-euk-diversity

  Public
  Clean version of repo for 2023 "euk-diversity" paper on taxonomic annotation of meta-omic sequences

  Jupyter Notebook

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 21, 2023Aug 21, 2023

• ehux_assembly_stats

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 1, 2023Aug 1, 2023

• EukHeist

  Public
  Jupyter Notebook

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  MIT License

  •66 forks•2525 stars•22 issues•00 pull requests•Updated Jun 20, 2023Jun 20, 2023

• jEUKebox

  Public
  Simulating microbial eukaryote communities to validate metatranscriptome assembly approaches.

  Jupyter Notebook

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  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 7, 2022Nov 7, 2022

• tara-download-snakemake

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 18, 2022May 18, 2022

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •3.9k3.9k forks•00 stars•00 issues•11 pull request•Updated Apr 5, 2022Apr 5, 2022

• 2022-metaT-m3-perspective

  Public
  Repository for 2022 m3 perspective paper on metatranscriptomics: code and figure resources.

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Feb 2, 2022Feb 2, 2022

• 2021-env-bioinformatics-snakemake

  Public
  Repository for the Snakemake lectures of the Fall 2021 Environmental Bioinformatics course.

  Python

  •22 forks•11 star•00 issues•00 pull requests•Updated Dec 1, 2021Dec 1, 2021

• cs-sea-catg

  Public
  Introduction to the computational side of the Alexander Lab - includes Poseidon information, an introduction to using Snakemake and bioinformatic command-line t…

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 28, 2021Aug 28, 2021

• 2021-Alexander-Tara-Paper

  Public
  Paper for Alexander 2021 Tara Euk Metagenomes

  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 26, 2021Jul 26, 2021

• 2021-TOPAZ-MAG-Figures

  Public
  Notebooks and tables required to generate figures from Alexander et al. 2021

  Jupyter Notebook

  •00 forks•00 stars•00 issues•11 pull request•Updated Jul 18, 2021Jul 18, 2021

• 2020-tara-mag-abund

  Public
  calculating mag abundance within metagenomes

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 16, 2021Jul 16, 2021

• 2021-McParland-Osmolytes-Paper

  Public
  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 2, 2021Jul 2, 2021

• 2021-06-14-whoipython

  Public
  The Carpentries Workshop Template

  HTML

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  Other

  •528528 forks•00 stars•00 issues•00 pull requests•Updated Jun 14, 2021Jun 14, 2021

• 2021-marine-osmolytes

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 14, 2021May 14, 2021

• BUSCO-MAG-Phylogeny

  Public
  Construction of concatenated gene tree from BUSCO genes

  Jupyter Notebook

  •33 forks•11 star•00 issues•00 pull requests•Updated Feb 9, 2021Feb 9, 2021

• eukhesit-annotate

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Dec 31, 2020Dec 31, 2020

• tara-euk-metaG

  Public
  Jupyter Notebook

  •

  MIT License

  •44 forks•44 stars•00 issues•00 pull requests•Updated Jul 31, 2020Jul 31, 2020

• 2020-06-16-whoipython

  Public
  Site for the June 2020 Software Carpentries Python Workshop for WHOI SSFs

  HTML

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  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 16, 2020Jun 16, 2020

• kobra-annotation

  Public
  snakemake enabled kegg annotation

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 6, 2020Jun 6, 2020

• slurm-useage-stats

  Public
  Mini-repo for investigating SLURM usage.

  Jupyter Notebook

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  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 4, 2020Jun 4, 2020

• keggannot

  Public
  KEGG annotation Python library

  Python

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  Other

  •33 forks•00 stars•00 issues•00 pull requests•Updated Apr 27, 2020Apr 27, 2020