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    • 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
      2410Updated Oct 30, 2024Oct 30, 2024
    • Gigwa2

      Public
      JavaScript
      GNU Affero General Public License v3.0
      89174Updated Oct 17, 2024Oct 17, 2024
    • 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
      28177Updated 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/).
      11902Updated Sep 15, 2024Sep 15, 2024
    • SynFlow

      Public
      JavaScript
      GNU General Public License v3.0
      0000Updated Sep 10, 2024Sep 10, 2024
    • metaXplor

      Public
      Store, share, explore, manipulate metagenomic data
      JavaScript
      GNU Affero General Public License v3.0
      1000Updated Sep 6, 2024Sep 6, 2024
    • rap-green

      Public
      Phylogenetic tree management, exploration and display package
      PHP
      GNU General Public License v3.0
      5600Updated Sep 2, 2024Sep 2, 2024
    • Interactive SouthGreen Staff Information page
      TeX
      GNU Lesser General Public License v3.0
      3100Updated Aug 21, 2024Aug 21, 2024
    • Web application to explore bacterial pangenomes
      HTML
      GNU General Public License v3.0
      1610Updated Jul 5, 2024Jul 5, 2024
    • 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.
      Python
      GNU General Public License v3.0
      11400Updated Jun 19, 2024Jun 19, 2024
    • Training Detection of SNP and Structural Variants using short and long reads
      0000Updated Jun 9, 2024Jun 9, 2024
    • Documentation related to the SouthGreen Platform - https://southgreenplatform.github.io/documentation/
      Creative Commons Attribution 4.0 International
      0100Updated 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
      61240Updated Mar 26, 2024Mar 26, 2024
    • HTML
      GNU General Public License v3.0
      0000Updated 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
      83610Updated Jan 31, 2024Jan 31, 2024
    • Jupyter Notebook
      MIT License
      2400Updated Nov 8, 2023Nov 8, 2023
    • App TrainingSV: Biosphere BASE environment for SV analysis using Jupyter
      Dockerfile
      MIT License
      0000Updated Oct 31, 2023Oct 31, 2023
    • Dockerfile
      MIT License
      1000Updated 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.
      Jupyter Notebook
      MIT License
      11142Updated Sep 13, 2023Sep 13, 2023
    • Training on Tools for Reproducible Research given by SouthGreen
      Python
      Creative Commons Attribution 4.0 International
      3360Updated Jun 15, 2023Jun 15, 2023
    • Jupyter Notebook
      MIT License
      1200Updated 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.
      Vue
      MIT License
      444100Updated Jun 7, 2023Jun 7, 2023
    • Python training given by SouthGreen (https://southgreenplatform.github.io/training_python)
      Creative Commons Attribution 4.0 International
      0200Updated Apr 21, 2023Apr 21, 2023
    • GeLoc

      Public
      Geloc provides convenient tools to visualised and download LRR genes family annotation data.
      JavaScript
      0100Updated Apr 11, 2023Apr 11, 2023
    • beegmac

      Public
      HTML
      0000Updated Feb 24, 2023Feb 24, 2023
    • R
      GNU General Public License v3.0
      0000Updated Feb 7, 2023Feb 7, 2023
    • Coding data, filtering, correcting GE, (partial ) imputing, a
      R
      GNU General Public License v3.0
      0000Updated Feb 7, 2023Feb 7, 2023
    • Perl
      GNU General Public License v3.0
      2000Updated Feb 7, 2023Feb 7, 2023
    • GeMo

      Public
      A mosaic genome painting tool for plant genomes
      JavaScript
      GNU General Public License v3.0
      11470Updated Feb 3, 2023Feb 3, 2023