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    37 repositories

    • ca-ocean-monitoring-map

      Public
      R
      •1•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • int-app

      Public
      application for visualization of CalCOFI integrated database
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • server

      Public
      calcofi.io server setup for R Shiny apps, RStudio IDE, R Plumber API, temporary PostGIS database, pg_tileserv
      Go
      •
      MIT License
      •0•2•6•0•Updated Apr 22, 2026Apr 22, 2026

    • api-h3t

      Public
      h3t tile server: base64-encoded SELECT against DuckDB → h3j JSON tiles for MapLibre. Pairs with mapgl::add_h3t_source().
      R
      •
      MIT License
      •0•1•0•0•Updated Apr 21, 2026Apr 21, 2026

    • apps

      Public
      Shiny apps for CalCOFI.io
      R
      •
      MIT License
      •0•0•10•0•Updated Apr 21, 2026Apr 21, 2026

    • calcofi4db

      Public
      R package for managing the integrated database
      R
      •
      Other
      •0•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • workflows

      Public
      helper scripts in R for common workflows
      HTML
      •
      MIT License
      •0•0•39•0•Updated Apr 8, 2026Apr 8, 2026

    • calcofi4r

      Public
      R package of data wrangling and visualization functions for working with CalCOFI data
      R
      •
      Other
      •2•0•5•0•Updated Apr 8, 2026Apr 8, 2026

    • erddap

      Public
      ERDDAP server configuration for CalCOFI (setup.xml, datasets.xml)
      0•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • Archived-eDNA-Sampling

      Public
      This protocol describes the methods used to sample preserved eDNA from archived biorepositories, such as ethanol-preserved bongo net tow samples.
      0•0•0•0•Updated Feb 28, 2026Feb 28, 2026

    • docs

      Public
      Help documentation for the constellation of webenized and workflow products (in bookdown)
      Mermaid
      •
      MIT License
      •0•0•2•0•Updated Feb 5, 2026Feb 5, 2026

    • eDNA-protocols

      Public
      Protocols for sampling, processing, and analysis of eDNA collected on CalCOFI cruises. All protocols are formatted according to guidelines from Better Biomolecu…
      obon-bebop
      obon-bebop
      Creative Commons Zero v1.0 Universal
      •1•2•0•0•Updated Dec 16, 2025Dec 16, 2025

    • MOSAIC_CTD_Sampling

      Public
      eDNA sampling protocol from CTD Niskin bottles.
      Creative Commons Zero v1.0 Universal
      •1•0•0•1•Updated Dec 16, 2025Dec 16, 2025

    • MOSAIC_Underway_Sampling

      Public
      Protocol for collecting eDNA samples from a ship's underway water system.
      Creative Commons Zero v1.0 Universal
      •2•0•0•3•Updated Dec 12, 2025Dec 12, 2025

    • Membrane-phenol-DNA-extraction

      Public
      This protocol describes the extraction of DNA from 47 mm filters stored without buffer using phenol:chloroform and an isopropanol precipitation.
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • eDNA_sampling_RREAS

      Public
      Sampling protocol based on the method developed for the NOAA Rockfish Recruitment and Ecosystem Assessment Survey (RREAS)
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • CalCOFI.github.io

      Public
      Default Github products website
      HTML
      •
      MIT License
      •0•0•3•0•Updated Oct 31, 2025Oct 31, 2025

    • Sterivex-phenol-DNA-extraction

      Public
      DNA extraction protocol from Sterivex filters using phenol:chloroform.
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • SaferSeafood

      Public
      Repository containing files and data for developing the R Shiny online application.
      HTML
      •1•0•5•0•Updated Sep 11, 2025Sep 11, 2025

    • 2025-capstone-calcofi

      Public
      MATLAB
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • MURI-MiFish-PCR-Protocol

      Public
      This protocol describes steps for performing PCR amplification of the 12S MiFish marker gene regions using eDNA extracted from sea water using a protocol develo…
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

    • MURI-d_loop-PCR-protocol

      Public
      PCR amplification protocol for the d-loop marker gene region targeting marine mammals
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • MBARI-62-MiFish-PCR-Protocol

      Public
      # MBARI60 MiFish PCR Protocol This repository contains the protocol for performing PCR amplification of the 12S MiFish marker gene region using eDNA extracted …
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • MBARI-60-MiFish-protocol

      Public
      This protocol describes steps for performing PCR for the 12S MiFish marker gene regions using eDNA extracted from sea water.
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • api

      Public
      Test application programming interface (API)
      R
      •0•1•3•0•Updated Apr 11, 2025Apr 11, 2025

    • marmam-app

      Public
      Collaboration of UCSB Data Science Capstone students and CalCOFI to generate RShiny App for visualizing CalCOFI marine mammal visual observations and eDNA detec…
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Dec 16, 2024Dec 16, 2024

    • CalCOFI_eDNA

      Public
      Data and code needed to conduct analysis for Marine Heatwave-Driven Impacts on Fish Assemblages Uncovered Through Archived DNA
      HTML
      •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

    • rCRUX

      Public
      A repository for my work on rCRUX
      noaa-omics-softwarenoaa-omics-studynoaa-omics-data
      noaa-omics-softwarenoaa-omics-studynoaa-omics-data
      R
      •
      GNU General Public License v3.0
      •8•12•13•0•Updated Jun 21, 2024Jun 21, 2024

    • CalCOFI_map

      Public
      Map of CalCOFI station grid
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • prj-mgt

      Public
      project management
      MIT License
      •0•0•6•0•Updated Feb 26, 2024Feb 26, 2024
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