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@AlexanderLabWHOI Alexander Lab @ WHOI

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    37 repositories

    • AlexanderLabWHOI.github.io

      Public
      Alexander Lab at Woods Hole Oceanographic Institution
      HTML
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • academic-kickstart

      Public
      Easily create a beautiful website using Academic and Hugo
      TeX
      •
      MIT License
      •6.4k•2•0•0•Updated Nov 1, 2024Nov 1, 2024

    • EUKulele

      Public
      Automatic eukaryotic taxonomic classification
      Python
      •
      MIT License
      •7•28•24•0•Updated Sep 25, 2024Sep 25, 2024

    • eukrhythmic

      Public
      A metatranscriptomic pipeline optimized for the study of microeukaryotes.
      Python
      •
      MIT License
      •3•15•18•3•Updated Sep 11, 2024Sep 11, 2024

    • 2024-Krinos-Ghux-Darwin

      Public
      Code for Krinos et al. G. huxleyi vital rates paper with Darwin model analysis
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 20, 2024Jun 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
      •1•0•0•0•Updated Aug 21, 2023Aug 21, 2023

    • ehux_assembly_stats

      Public
      Shell
      •0•0•0•0•Updated Aug 1, 2023Aug 1, 2023

    • EukHeist

      Public
      Jupyter Notebook
      •
      MIT License
      •5•23•1•0•Updated Jun 20, 2023Jun 20, 2023

    • jEUKebox

      Public
      Simulating microbial eukaryote communities to validate metatranscriptome assembly approaches.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 7, 2022Nov 7, 2022

    • tara-download-snakemake

      Public
      Python
      •0•0•0•0•Updated May 18, 2022May 18, 2022

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.3k•0•0•1•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
      •0•0•0•0•Updated Feb 2, 2022Feb 2, 2022

    • 2021-env-bioinformatics-snakemake

      Public
      Repository for the Snakemake lectures of the Fall 2021 Environmental Bioinformatics course.
      Python
      •2•1•0•0•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 tools, and basic data analysis skills. Much of this co-opted from or duplicated to the Alexander Lab blog.
      MIT License
      •0•2•0•0•Updated Aug 28, 2021Aug 28, 2021

    • 2021-Alexander-Tara-Paper

      Public
      Paper for Alexander 2021 Tara Euk Metagenomes
      TeX
      •0•0•0•0•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
      •0•0•0•1•Updated Jul 18, 2021Jul 18, 2021

    • 2020-tara-mag-abund

      Public
      calculating mag abundance within metagenomes
      Jupyter Notebook
      •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021

    • 2021-McParland-Osmolytes-Paper

      Public
      TeX
      •0•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • 2021-06-14-whoipython

      Public
      The Carpentries Workshop Template
      HTML
      •
      Other
      •522•0•0•0•Updated Jun 14, 2021Jun 14, 2021

    • 2021-marine-osmolytes

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 14, 2021May 14, 2021

    • BUSCO-MAG-Phylogeny

      Public
      Construction of concatenated gene tree from BUSCO genes
      Jupyter Notebook
      •3•0•0•0•Updated Feb 9, 2021Feb 9, 2021

    • eukhesit-annotate

      Public
      Python
      •1•0•0•0•Updated Dec 31, 2020Dec 31, 2020

    • tara-euk-metaG

      Public
      Jupyter Notebook
      •
      MIT License
      •4•4•0•0•Updated Jul 31, 2020Jul 31, 2020

    • 2020-06-16-whoipython

      Public
      Site for the June 2020 Software Carpentries Python Workshop for WHOI SSFs
      HTML
      •
      Other
      •0•0•0•0•Updated Jun 16, 2020Jun 16, 2020

    • kobra-annotation

      Public
      snakemake enabled kegg annotation
      Python
      •0•0•0•0•Updated Jun 6, 2020Jun 6, 2020

    • slurm-useage-stats

      Public
      Mini-repo for investigating SLURM usage.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 4, 2020Jun 4, 2020

    • keggannot

      Public
      KEGG annotation Python library
      Python
      •
      Other
      •3•0•0•0•Updated Apr 27, 2020Apr 27, 2020

    • areyouok-mer

      Public
      Directory for the Snakemake workflow for checking sourmash similarities of protists
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Apr 25, 2020Apr 25, 2020

    • BVCNSample

      Public
      The sample project for the BVCN reproducibility challenge, which is based on a paper by Long et al. published in BMC Genomics in 2013.
      MIT License
      •1•0•0•0•Updated Apr 16, 2020Apr 16, 2020

    • MAGpy

      Public
      Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
      Jupyter Notebook
      •30•0•0•0•Updated Feb 6, 2020Feb 6, 2020