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    23 repositories

    • armbrustlab.github.io

      Public
      HTML
      •
      MIT License
      •5•2•0•0•Updated Oct 4, 2024Oct 4, 2024

    • NPac_euk_gene_catalog

      Public
      North Pacific eukaryotic metatranscriptome assemblies and annotations
      Shell
      •
      MIT License
      •0•1•0•0•Updated Sep 5, 2024Sep 5, 2024

    • marferret

      Public
      Code repository for collection, ingestion, and processing of genomic and transcriptomic sequence data into a reproducible reference sequence database
      Python
      •
      MIT License
      •0•2•0•0•Updated Feb 29, 2024Feb 29, 2024

    • seaflow-transfer

      Public
      SeaFlow data transfer tool
      Go
      •
      MIT License
      •0•1•1•2•Updated Mar 7, 2023Mar 7, 2023

    • Thaps_Catl

      Public
      R
      •0•0•0•0•Updated Jun 24, 2022Jun 24, 2022

    • trophic-mode-ml

      Public
      Accompanying code for 'The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.'
      HTML
      •
      MIT License
      •0•2•0•0•Updated Feb 18, 2022Feb 18, 2022

    • seaflow-realtime-deployment

      Public
      Shell
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 7, 2021Sep 7, 2021

    • cruisereplay

      Public
      Replay historical data feeds for a research cruise
      Go
      •
      MIT License
      •0•0•0•0•Updated Jul 13, 2021Jul 13, 2021

    • diel_eukaryotes

      Public
      Code repository for 'Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre'
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 2, 2021Jul 2, 2021

    • gradients-amplicon

      Public
      Sharing is caring.
      R
      •0•0•0•0•Updated Aug 11, 2020Aug 11, 2020

    • manta

      Public
      Microbial Assemblage Normalized Transcript Analysis
      R
      •
      Other
      •0•0•0•0•Updated Dec 16, 2019Dec 16, 2019

    • moduledetection-evaluation

      Public
      Python
      •12•0•0•0•Updated Jul 18, 2019Jul 18, 2019

    • matrix_model_matlab

      Public
      Prepping SeaFlow data and using it in the Hunter-Cevera 2-population matrix growth model
      MATLAB
      •1•0•0•0•Updated Apr 5, 2019Apr 5, 2019

    • SEAStAR

      Public
      SEAStAR is a package of tools supporting the construction of complete analysis pipelines for next-generation (Illumina®, SOLiD™) sequencing data generated from environmental samples.
      C
      •
      GNU General Public License v3.0
      •2•13•1•0•Updated Feb 27, 2019Feb 27, 2019

    • seaflowviz3

      Public
      Web visualizations for SeaFlow data
      1•1•0•0•Updated Oct 2, 2018Oct 2, 2018

    • ssPopModel_respiration

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 8, 2018Aug 8, 2018

    • global_thaps_clones

      Public
      TeX
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 12, 2018Jul 12, 2018

    • NWPac_amplicon

      Public
      Workup of 16S/18S data from three cruises in the NW Pacific
      Shell
      •
      MIT License
      •2•0•0•0•Updated May 30, 2018May 30, 2018

    • opedia

      Public
      HTML
      •6•0•0•0•Updated May 29, 2018May 29, 2018

    • clusterPop

      Public
      clusterPop is a R package that performs real-time clustering analysis and visualization of measured phytoplankton populations using a modified version of our software packge flowPhyto.
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 27, 2018Mar 27, 2018

    • cytDiv

      Public
      cytoDiv is a R function that calculates ecological diversity indices for a microbial community based on its bio-optical properties measured at the single cell level by flow cytometry. The indices express the organization and structure of a community, its richness in physiological and genetic variations. The equations used to calculate the indice…
      reproducible-researchoceanographyseaflowflow-cytometry
      R
      •
      MIT License
      •2•2•0•1•Updated Mar 27, 2018Mar 27, 2018

    • flowPhyto

      Public
      flowPhyto is a package for the R statistical programming language that uses automated computational methods (flowClust and flowMeans) to cluster phytoplankton populations, perform aggregate statistics and create maps of phytoplankton distribution from georeferenced flow cytometry data. For more details, see Ribalet, F., Schruth, D., and Armbrust…
      R
      •
      MIT License
      •1•3•0•0•Updated Mar 27, 2018Mar 27, 2018

    • seaflowviz2

      Public
      SeaFlow realtime data dashboard with Meteor
      JavaScript
      •0•3•0•0•Updated Aug 11, 2015Aug 11, 2015