Pinned Repositories
2021-06-14-whoipython
The Carpentries Workshop Template
2021-env-bioinformatics-snakemake
Repository for the Snakemake lectures of the Fall 2021 Environmental Bioinformatics course.
2021-marine-osmolytes
academic-kickstart
Easily create a beautiful website using Academic and Hugo
cs-sea-catg
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.
EukHeist
eukrhythmic
A metatranscriptomic pipeline optimized for the study of microeukaryotes.
EUKulele
Automatic eukaryotic taxonomic classification
gene-finder
Snakemake for hmmer searches
tara-euk-metaG
Alexander Lab @ WHOI's Repositories
AlexanderLabWHOI/EUKulele
Automatic eukaryotic taxonomic classification
AlexanderLabWHOI/EukHeist
AlexanderLabWHOI/eukrhythmic
A metatranscriptomic pipeline optimized for the study of microeukaryotes.
AlexanderLabWHOI/tara-euk-metaG
AlexanderLabWHOI/academic-kickstart
Easily create a beautiful website using Academic and Hugo
AlexanderLabWHOI/cs-sea-catg
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.
AlexanderLabWHOI/2021-env-bioinformatics-snakemake
Repository for the Snakemake lectures of the Fall 2021 Environmental Bioinformatics course.
AlexanderLabWHOI/2020-06-16-whoipython
Site for the June 2020 Software Carpentries Python Workshop for WHOI SSFs
AlexanderLabWHOI/2021-06-14-whoipython
The Carpentries Workshop Template
AlexanderLabWHOI/2021-Alexander-Tara-Paper
Paper for Alexander 2021 Tara Euk Metagenomes
AlexanderLabWHOI/2021-marine-osmolytes
AlexanderLabWHOI/2021-McParland-Osmolytes-Paper
AlexanderLabWHOI/2022-metaT-m3-perspective
Repository for 2022 m3 perspective paper on metatranscriptomics: code and figure resources.
AlexanderLabWHOI/2020-tara-mag-abund
calculating mag abundance within metagenomes
AlexanderLabWHOI/2021-TOPAZ-MAG-Figures
Notebooks and tables required to generate figures from Alexander et al. 2021
AlexanderLabWHOI/2023-euk-diversity
Clean version of repo for 2023 "euk-diversity" paper on taxonomic annotation of meta-omic sequences
AlexanderLabWHOI/2024-Krinos-Ghux-Darwin
Code for Krinos et al. G. huxleyi vital rates paper with Darwin model analysis
AlexanderLabWHOI/AlexanderLabWHOI.github.io
Alexander Lab at Woods Hole Oceanographic Institution
AlexanderLabWHOI/areyouok-mer
Directory for the Snakemake workflow for checking sourmash similarities of protists
AlexanderLabWHOI/bioconda-recipes
Conda recipes for the bioconda channel.
AlexanderLabWHOI/BUSCO-MAG-Phylogeny
Construction of concatenated gene tree from BUSCO genes
AlexanderLabWHOI/BVCNSample
The sample project for the BVCN reproducibility challenge, which is based on a paper by Long et al. published in BMC Genomics in 2013.
AlexanderLabWHOI/ehux_assembly_stats
AlexanderLabWHOI/eukhesit-annotate
AlexanderLabWHOI/jEUKebox
Simulating microbial eukaryote communities to validate metatranscriptome assembly approaches.
AlexanderLabWHOI/keggannot
KEGG annotation Python library
AlexanderLabWHOI/kobra-annotation
snakemake enabled kegg annotation
AlexanderLabWHOI/MAGpy
Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
AlexanderLabWHOI/slurm-useage-stats
Mini-repo for investigating SLURM usage.
AlexanderLabWHOI/tara-download-snakemake