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@SouthGreenPlatform

South Green Bioinformatics platform

Public repostiory of code for bioinformatics applications developed in the South Green Bioinformatics platform

Pinned

  1. culebrONT Public

    A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.

    Python 30 8

  2. tutorials Public

    An open resource material for people who wish to know about bioinformatics specially users of the Southgreen Platform (https://southgreenplatform.github.io/tutorials/). It contains tips, tutorials …

    4 4

  3. 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/).

    8 11

  4. 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-…

    Vue 34 4

  5. Gigwa2 Public

    JavaScript 9 7

  6. rap-green Public

    Phylogenetic tree management, exploration and display package

    PHP 4 3

Repositories

  • GeMo Public

    A mosaic genome painting tool for plant genomes

    JavaScript 7 GPL-3.0 0 7 0 Updated Feb 3, 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 34 MIT 4 7 (1 issue needs help) 0 Updated Feb 2, 2023
  • 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 7 GPL-3.0 3 13 7 Updated Feb 1, 2023
  • R 0 GPL-3.0 0 0 0 Updated Jan 31, 2023
  • Curation-GBS-data Public

    Coding data, filtering, correcting GE, (partial ) imputing, a

    R 0 GPL-3.0 0 0 0 Updated Jan 31, 2023
  • PanExplorer_workflow Public

    Snakemake worklow for bacterial pan-genome analysis. It can be run in the back-end of PanExplorer web application

    Perl 1 GPL-3.0 1 0 0 Updated Jan 31, 2023
  • 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 4 GPL-3.0 5 4 0 Updated Jan 26, 2023
  • Gigwa2 Public
    JavaScript 9 AGPL-3.0 7 13 1 Updated Jan 25, 2023
  • PanExplorer Public

    Web application to explore bacterial pangenomes

    HTML 7 GPL-3.0 1 0 0 Updated Jan 16, 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 11 MIT 1 4 1 Updated Jan 2, 2023

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