South Green Bioinformatics platform

Repositories

• AgroLD_ETL

  ETL for RDF data lifting for the AgroLD project. Python packages for GFF, VCF, GAF and specific plant databases.

  etl rdf vcf ontologies rdf-data gff gaf
  Python GPL-3.0 0 0 22 0 Updated Dec 3, 2020

• trainings

  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/).

  linux cluster ngs toggle galaxy
  8 3 0 1 Updated Dec 3, 2020

• rap-green

  Phylogenetic tree management, exploration and display package
  PHP 1 1 0 0 Updated Dec 1, 2020

• CulebrONT_pipeline

  A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.
  Python GPL-3.0 0 14 0 0 Updated Nov 30, 2020

• Gigwa2ServiceImpl
  Java AGPL-3.0 0 0 0 0 Updated Nov 26, 2020

• Gigwa2
  Java 0 4 4 1 Updated Nov 26, 2020

• Mgdb2BrapiV2Impl

  Forked from GuilhemSempere/BrAPIv2Impl
  Java 1 0 0 0 Updated Nov 26, 2020

• Mgdb2
  Java AGPL-3.0 0 0 0 3 Updated Nov 26, 2020

• AgroLD_webappV2

  New version of the AgroLD Web app
  JavaScript 0 0 2 0 Updated Nov 19, 2020

• metaXplor

  metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing and exploring metagenomic data . Being based on a flexible NoSQL data model, it has very few constraints regarding dataset contents, and thus proves useful for handling outputs from both shot-gun and metabarcoding techniques. By supporting incremental …
  JavaScript 0 0 0 1 Updated Nov 13, 2020

• metaXplorDB

  MongoDB persistence layer for metaXplor
  Java 0 0 0 0 Updated Nov 13, 2020

• role_manager

  Generic web tool for managing user roles using Spring Security
  Java AGPL-3.0 0 0 0 0 Updated Nov 13, 2020

• AgroLD_webapp

  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 2 2 10 4 Updated Oct 13, 2020

• Gigwa2ServiceInterface
  Java AGPL-3.0 0 0 0 2 Updated Oct 13, 2020

• VcfHunter
  Python GPL-3.0 4 2 1 0 Updated Oct 7, 2020

• Mgdb2BrapiImpl
  Java AGPL-3.0 0 0 0 1 Updated Sep 4, 2020

• DataViz
  JavaScript 0 0 0 4 Updated Aug 27, 2020

• galaxy
  Ruby 0 0 0 1 Updated Aug 8, 2020

• PyRice

  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.

  rice bioinformatics-analysis
  Jupyter Notebook MIT 1 6 1 2 Updated Aug 7, 2020

• TOGGLE-DEV

  Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis (development repository)

  workflow pipeline ngs generic-ngs-analyses
  Perl GPL-3.0 5 2 0 0 Updated Aug 4, 2020

• TOGGLE

  Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

  workflow pipeline ngs-analysis generic-ngs-analyses
  Perl GPL-3.0 5 19 1 0 Updated Aug 4, 2020

• duplicationDetector
  Perl GPL-3.0 0 2 0 0 Updated Aug 4, 2020

• beegmac
  HTML 0 0 0 0 Updated Jul 23, 2020

• mgdb

  Mongo Genotyping DataBase
  Java 0 0 0 1 Updated Jun 15, 2020

• OpalClient

  Customized Java client code for invoking Opal Toolkit services
  Java 0 0 0 0 Updated May 13, 2020

• tutorials

  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 on bioinformatics analysis and softwares.

  bioinformatics tutorials
  4 4 0 0 Updated Apr 17, 2020

• Mgdb2Export
  Java AGPL-3.0 0 0 0 0 Updated Mar 25, 2020

• mgdb_export

  Export handlers for mgdb
  Java 1 0 0 0 Updated Mar 16, 2020

• GalaxyHomepageIRD
  JavaScript 0 0 0 3 Updated Feb 26, 2020

• singularityRecipeFiles

  This repository provides a series of Singularity recipe files used to easily deploy numerous bioinformatics softwares through containers.All these Singularity recipes are ready to be used by the bioinformatics community and have been developed to be integrated into the workflow manager TOGGLe http://toggle.southgreen.fr.

  singularity-containers recipe-files
  0 0 0 0 Updated Jan 27, 2020