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    50 repositories

    • PanExplorer_workflow

      Public
      Snakemake worklow for bacterial pan-genome analysis. It can be run in the back-end of PanExplorer web application
      Perl
      •
      GNU General Public License v3.0
      •2•4•1•0•Updated Oct 30, 2024Oct 30, 2024

    • Gigwa2

      Public
      JavaScript
      •
      GNU Affero General Public License v3.0
      •8•9•17•4•Updated Oct 17, 2024Oct 17, 2024

    • AgroLD_webapp

      Public
      AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. The aim of the Agronomic Linked Data (AgroLD) project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.
      JavaScript
      •
      GNU General Public License v3.0
      •2•8•17•7•Updated Sep 27, 2024Sep 27, 2024

    • trainings

      Public
      The South Green platform has conducted a series of training courses for several years and this github repository gives access to all trainings (https://southgreenplatform.github.io/trainings/).
      linuxclusterngstogglegalaxy
      11•9•0•2•Updated Sep 15, 2024Sep 15, 2024

    • SynFlow

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • metaXplor

      Public
      Store, share, explore, manipulate metagenomic data
      JavaScript
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • rap-green

      Public
      Phylogenetic tree management, exploration and display package
      PHP
      •
      GNU General Public License v3.0
      •5•6•0•0•Updated Sep 2, 2024Sep 2, 2024

    • staff-info

      Public
      Interactive SouthGreen Staff Information page
      TeX
      •
      GNU Lesser General Public License v3.0
      •3•1•0•0•Updated Aug 21, 2024Aug 21, 2024

    • PanExplorer

      Public
      Web application to explore bacterial pangenomes
      HTML
      •
      GNU General Public License v3.0
      •1•6•1•0•Updated Jul 5, 2024Jul 5, 2024

    • AgroLD_ETL

      Public
      AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. AgroLD ETL is the Python packages developed to transform plant datasets in RDF. Packages are developped for data standards such as GFF,GAF, VCF and specific plant databases.
      etlvcfontologiesrdf-datagffgafrdf
      Python
      •
      GNU General Public License v3.0
      •1•1•40•0•Updated Jun 19, 2024Jun 19, 2024

    • training_SV_teaching

      Public
      Training Detection of SNP and Structural Variants using short and long reads
      0•0•0•0•Updated Jun 9, 2024Jun 9, 2024

    • documentation

      Public
      Documentation related to the SouthGreen Platform - https://southgreenplatform.github.io/documentation/
      documentationbioinformatics
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Mar 27, 2024Mar 27, 2024

    • VcfHunter

      Public
      VcfExplorer regroups several programs which principal aims are to map DNA and RNAseq data onto reference genome sequence, perform variant calling, manipulate vcf files, perform chromosome painting of accessions based on the contribution of ancestral groups, select marker for genetic map analysis and perform pairwise chromosome linkage of ordered…
      Python
      •
      GNU General Public License v3.0
      •6•12•4•0•Updated Mar 26, 2024Mar 26, 2024

    • Galaxy-docker-rnaseq

      Public
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • culebrONT

      Public archive
      A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.
      Python
      •
      GNU General Public License v3.0
      •8•36•1•0•Updated Jan 31, 2024Jan 31, 2024

    • training_ONT_teaching

      Public
      Jupyter Notebook
      •
      MIT License
      •2•4•0•0•Updated Nov 8, 2023Nov 8, 2023

    • training_SV_VM

      Public
      App TrainingSV: Biosphere BASE environment for SV analysis using Jupyter
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • training_ONT_VM

      Public
      Dockerfile
      •
      MIT License
      •1•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • PyRice

      Public
      PyRice is an API to access some Rice public databases at the same time with consistent output. PyRice design is modular and implements a smart query system which fits the computing resources to optimize the query speed.
      ricebioinformatics-analysis
      Jupyter Notebook
      •
      MIT License
      •1•11•4•2•Updated Sep 13, 2023Sep 13, 2023

    • training_reproducible_research

      Public
      Training on Tools for Reproducible Research given by SouthGreen
      gitsnakemakenotebookcontainercondarmarkdownquarto
      Python
      •
      Creative Commons Attribution 4.0 International
      •3•3•6•0•Updated Jun 15, 2023Jun 15, 2023

    • training_bacterial_comparative_genomics

      Public
      Trainings for Bacterial Comparative Genomics (https://southgreenplatform.github.io/training_bacterial_comparative_genomics/)
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Jun 9, 2023Jun 9, 2023

    • panache

      Public
      Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.
      javascriptpangenomevizualisation
      Vue
      •
      MIT License
      •4•44•10•0•Updated Jun 7, 2023Jun 7, 2023

    • training_advanced_linux_and_bash_initiation

      Public
      (https://southgreenplatform.github.io/training_advanced_linux_and_bash_initiation)
      Other
      •0•1•0•0•Updated May 10, 2023May 10, 2023

    • training_python

      Public
      Python training given by SouthGreen (https://southgreenplatform.github.io/training_python)
      pythontraining
      Creative Commons Attribution 4.0 International
      •0•2•0•0•Updated Apr 21, 2023Apr 21, 2023

    • GeLoc

      Public
      Geloc provides convenient tools to visualised and download LRR genes family annotation data.
      dataviz
      JavaScript
      •0•1•0•0•Updated Apr 11, 2023Apr 11, 2023

    • beegmac

      Public
      HTML
      •0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • Myrtaceae-RNASeq-scripts

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 7, 2023Feb 7, 2023

    • Curation-GBS-data

      Public
      Coding data, filtering, correcting GE, (partial ) imputing, a
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 7, 2023Feb 7, 2023

    • Workflow-snakemake-capture

      Public
      Perl
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Feb 7, 2023Feb 7, 2023

    • GeMo

      Public
      A mosaic genome painting tool for plant genomes
      visualizationbioinformaticswebplantsgenomesbioinformatics-scriptskaryotype
      JavaScript
      •
      GNU General Public License v3.0
      •1•14•7•0•Updated Feb 3, 2023Feb 3, 2023