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@CefasRepRes Centre for Environment Fisheries and Aquaculture Science (Cefas)

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    79 repositories

    • alewijnse-top-length-at-maturity

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

    • NEMO4.0-FABM

      Public
      Fortran
      •
      Other
      •1•1•2•0•Updated Apr 23, 2026Apr 23, 2026

    • MixME

      Public
      R package for Mixed-fishery Multi-stock Evaluation
      R
      •1•1•4•0•Updated Apr 10, 2026Apr 10, 2026

    • cefasRBR

      Public
      R package for working with RBR Profiling instruments
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • flowcytometertool

      Public
      Python
      •
      Other
      •0•2•26•0•Updated Mar 31, 2026Mar 31, 2026

    • marsh-salmon-habitat-carryovereffects

      Public
      code to accompany paper
      HTML
      •
      Other
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • Cefas_UEA_RCourse2025

      Public
      Repo for the Cefas UEA R Course
      R
      •
      Other
      •2•0•0•1•Updated Mar 18, 2026Mar 18, 2026

    • QuinCe

      Public
      QuinCe is an online tool for processing and quality control of data from scientific instruments, with a primary focus on oceanic data.
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • cefas-pi-10-edge-ai

      Public
      Edge AI system used on board the Cefas Endeavour for plankton inference
      Python
      •
      Other
      •1•1•2•0•Updated Feb 23, 2026Feb 23, 2026

    • shipwreck-oil-detection-colab

      Public
      Google Colab tool for detecting oil spills from historical shipwrecks
      Jupyter Notebook
      •
      MIT License
      •0•0•3•0•Updated Feb 20, 2026Feb 20, 2026

    • uk-marine-ornamentals

      Public
      Code for data cleaning and analysis of marine ornamental imports into the UK
      R
      •
      Other
      •0•0•0•0•Updated Feb 6, 2026Feb 6, 2026

    • eDNA-spatial-bound-paper

      Public
      Code used in Silva et al 2025. Frontiers in Marine Science. Modelling the spatial bound of an eDNA signal in the marine environment – the effect of local condit…
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • MDR_searcher_public

      Public
      Public fork of MDR search app
      Python
      •
      Other
      •1•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • aquanet-mod

      Public
      R scripts for AquaNet-Mod (The Aquaculture Disease Network Model).
      R
      •
      Other
      •0•1•2•0•Updated Jan 21, 2026Jan 21, 2026

    • aquanet

      Public
      R package containing the functions required to run AquaNet-Mod (The Aquaculture Disease Network Model).
      r-package
      r-package
      R
      •
      Other
      •0•2•0•0•Updated Jan 21, 2026Jan 21, 2026

    • cytosense_to_ecotaxa_pipeline

      Public
      Generate TSV file for Ecotaxa from Cytosense CYZ file
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • COMPEAT-updater

      Public
      OPSAR IA COMPEAT udpater code that updates COMP inputs from SQL and re-runs the assessment code
      R
      •
      Creative Commons Zero v1.0 Universal
      •9•0•0•0•Updated Jan 10, 2026Jan 10, 2026

    • resample-extremes

      Public
      Python code to resample mutli-resolution timeseries containing extremes
      Python
      •
      Other
      •1•0•0•0•Updated Dec 31, 2025Dec 31, 2025

    • EcoEnsemble

      Public
      R package for implementing the ensemble framework for combining ecosystem models.
      C++
      •
      GNU General Public License v3.0
      •4•2•0•1•Updated Sep 26, 2025Sep 26, 2025

    • Cefas.MDR.OgrEnvironmentalDataRetrieval

      Public
      OGC Environment Data Retrieval API
      C#
      •0•1•0•0•Updated Sep 19, 2025Sep 19, 2025

    • FUME

      Public
      Calculates the Forel-Ule Index of water quality from surface reflectances. Works with point and image data.
      Jupyter Notebook
      •
      Other
      •6•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • gene-pools-paper

      Public
      Pre-processing scripts for manuscript for gene pools project.
      0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • CO_AMM15

      Public
      Coastal Ocean (CO) configuration of the Atlantic Margin Model (1.5 km resolution)
      Fortran
      •1•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • CO_AMM7

      Public
      AMM7 configuration for testing various vertical coordinate options
      Fortran
      •2•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • TawTorridgeCatchmentData

      Public
      Data repository for SWAT model catchment data from the Taw and Torridge catchments
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 4, 2025Jul 4, 2025

    • agriforwards-summer-school-2022

      Public
      Planning for the UEA / Cefas AgriFoRwArdS summer school 2022
      Jupyter Notebook
      •9•7•0•1•Updated Jul 3, 2025Jul 3, 2025

    • ICES-VMS-and-Logbook-Data-Call_Cefas

      Public
      repository for repsonse to ICES VMS& LOGBOOK DATACALL adapated to Cefas requirements
      R
      •
      GNU General Public License v3.0
      •5•0•12•0•Updated Jul 1, 2025Jul 1, 2025

    • salmon-rod-exploitation

      Public
      Article and analysis code for ICES JMS paper "Estimation of returning Atlantic salmon stock from rod exploitation rate for principal salmon rivers in England & …
      R
      •
      Other
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • ices_vms_logbook_datacall

      Public
      Code to produce the datasets required for the annual ICES VMS/Logbook datacall
      R
      •0•1•2•1•Updated Jun 10, 2025Jun 10, 2025

    • mizerShiny

      Public
      mizerShiny is a frontend to mizer models that allows interactive simulation of mizer models.
      R
      •
      MIT License
      •3•0•0•0•Updated Jun 5, 2025Jun 5, 2025
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