Repositories list

• edentity-sequencer-qc

  Public
  scripts for comparing sequencer outputs

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• sdmdl

  Public
  Species Distribution Modelling using Deep Learning

  biodiversity-patternsecological-niche-modellingdl-sdm+ 1deep-learning

  Python

  •

  MIT License

  •11•24•4•21•Updated Nov 2, 2024Nov 2, 2024

• edentity-metabarcoding-phylodiv

  Public
  Shell scripts for prototyping a QIIME2

  Apache License 2.0

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• barcode_validator

  Public
  Standardized validation of barcodes

  Python

  •

  Apache License 2.0

  •4•1•3•3•Updated Oct 17, 2024Oct 17, 2024

• barcode-constrained-phylogeny

  Public
  Pipeline for building topologically-constrained phylogenies from DNA barcode data

  phylogeneticsphylogenetic-diversitymetabarcoding+ 2phylogenetic-placementdna-barcoding

  Python

  •

  Apache License 2.0

  •3•2•21•0•Updated Sep 8, 2024Sep 8, 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

• 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 May 15, 2024May 15, 2024

• barcode-phylogenetic-diversity

  Public
  Repository for experiments with QIIME-based alpha/beta PD metrics

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 29, 2024Apr 29, 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

  •14•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

  rhpcmetabarcoding+ 1arise

  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•1•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

• mebioda

  Public
  Course repository for Methods in Biodiversity Analysis

  HTML

  •

  MIT License

  •82•21•7•0•Updated May 24, 2023May 24, 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•1•0•0•Updated Feb 15, 2023Feb 15, 2023

• sysbio-independent-contrasts

  Public
  Demonstration of independent contrasts calculations for spider length dimorphism

  MIT License

  •0•0•0•0•Updated Nov 29, 2022Nov 29, 2022

• galaxy-tool-add-metadata-otutable

  Public
  Python

  •0•0•0•0•Updated Nov 16, 2022Nov 16, 2022