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    177 repositories

    • barcode_validator

      Public
      Standardized validation of barcodes
      Python
      •
      Apache License 2.0
      •5•1•2•0•Updated Feb 10, 2025Feb 10, 2025

    • edentity-metabarcoding-phylodiv

      Public
      Shell scripts for prototyping a QIIME2
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.4k•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • barcode-constrained-phylogeny

      Public
      Pipeline for building topologically-constrained phylogenies from DNA barcode data
      phylogeneticsphylogenetic-diversitymetabarcodingphylogenetic-placementdna-barcoding
      Python
      •
      Apache License 2.0
      •3•2•21•1•Updated Feb 4, 2025Feb 4, 2025

    • barcode-phylogenetic-diversity

      Public
      Repository for experiments with QIIME-based alpha/beta PD metrics
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • sdmdl

      Public
      Species Distribution Modelling using Deep Learning
      biodiversity-patternsecological-niche-modellingdl-sdmdeep-learning
      Python
      •
      MIT License
      •11•24•4•21•Updated Jan 31, 2025Jan 31, 2025

    • barcode-classify-protax-fungi

      Public
      Profiling PROTAX-fungi for quick and coarse classification of ITS metabarcoding reads
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • edentity-sequencer-qc

      Public
      scripts for comparing sequencer outputs
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • mebioda

      Public
      Course repository for Methods in Biodiversity Analysis
      HTML
      •
      MIT License
      •82•21•7•0•Updated Nov 28, 2024Nov 28, 2024

    • BGE-gaplist

      Public
      Pipeline for generating and updating the BGE gap list
      Perl
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • evobio2

      Public
      EvBio2 UL computer practicum
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • DWCAConfig

      Public
      DWCA Configuratie bestanden om data te downloaden uit ES (NBA)
      Shell
      •2•1•1•0•Updated Aug 7, 2024Aug 7, 2024

    • barcode-classify-transformer

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • mycodiversity

      Public
      Pipelines for analyzing fungal diversity
      Python
      •
      MIT License
      •1•1•0•3•Updated May 26, 2024May 26, 2024

    • galaxy-tool-lca

      Public
      Python
      •2•3•1•0•Updated Apr 9, 2024Apr 9, 2024

    • DNABERT_S

      Public
      DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
      Python
      •20•0•0•0•Updated Mar 21, 2024Mar 21, 2024

    • galaxy-tool-make-otu-table

      Public
      Python
      •0•0•0•0•Updated Mar 21, 2024Mar 21, 2024

    • browbrow

      Public
      Brownian motion in a browser window
      Creative Commons Zero v1.0 Universal
      •0•0•4•0•Updated Feb 28, 2024Feb 28, 2024

    • galaxy-pipeline-hybseq

      Public
      End-to-end implementation of HybSeq analysis in Naturalis's Galaxy portal
      Python
      •
      MIT License
      •1•0•1•0•Updated Feb 19, 2024Feb 19, 2024

    • galaxy-tool-taxonmatcher

      Public
      Find for your input taxonomy the taxonomy from an other database
      Python
      •0•3•1•0•Updated Jan 31, 2024Jan 31, 2024

    • bioblend-test

      Public
      Example implementation of bioblend galaxy client
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • snakemake-parallel-test

      Public
      Perl
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 15, 2023Dec 15, 2023

    • arise-metabarcoding-biodiversity

      Public
      ARISE metabarcoding
      rhpcmetabarcodingarise
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

    • galaxy-tool-BLAST

      Public
      A new tool and wrapper for the identification with blastn
      Python
      •1•0•2•0•Updated Nov 20, 2023Nov 20, 2023

    • comp-genome-mammals-cmah

      Public
      Repository for the comparative analysis of CMAH inactivation in Mammalian genomes
      Shell
      •
      MIT License
      •0•0•2•0•Updated Nov 14, 2023Nov 14, 2023

    • mtdna-reference-database

      Public
      Reference database of panels of genomes for population-level aDNA identification
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 16, 2023Aug 16, 2023

    • arise-soil-pilot-analysis

      Public
      Repository for statistical analysis of spatial structure in the ARISE soil pilot
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

    • PROTAX

      Public
      Software for training probabilistic taxonomic classifier PROTAX
      Perl
      •2•0•0•0•Updated May 16, 2023May 16, 2023

    • galaxy-tool-cutadapt

      Public
      Python
      •0•0•0•0•Updated Apr 19, 2023Apr 19, 2023

    • seshat-trait-data-domesticates

      Public
      Repository for aggregating comparative trait data for Ungulates and Poaceae and preparing for submission to the SESHAT database
      Other
      •0•2•0•0•Updated Feb 15, 2023Feb 15, 2023