Wageningen UR Plant Breeding

pedigreeSim

PedigreeSim is software that generates simulated genetic marker data of individuals in pedigreed populations. A population can consist of either diploid or tetraploid individuals. PedigreeSim can simulate meioses with or without chiasma interference, and in tetraploids it can simulate meioses with two bivalents or one quadrivalent per set of hom(oe)ologous chromosomes. Also varying probabilities of preferential versus random pairing of chromosomes can be simulated, allowing to simulate amphidiploids as well as autotetraploids and intermediate forms.

Pedimap

Pedimap: software for the visualization of genetic and phenotypic data in pedigrees

QTM

QTLTableMiner++ tool for mining tables in scientific articles

chebi2gene

jChebi2gene

Java library to automatically link a chebi compound/identifier to a metabolic pathway or genes from the tomato genome.

MySQLdbCompare

Compare copies of MySQL db schemas

AdvBioInfo_2012

Advanced Bioinformatics Course 2012

BreeDB-Lite

BreeDB is a relational database which aims to support breeding for quantitative agronomical traits. The database can be explored through a web-based interface, which offers tools to present basic statistical overviews such as box plots , histograms, but also multivariate tools. Graphical genotyping tools are available to show molecular marker data and QTL data in relation to genetic linkage maps. In addition, photos of each accession can be shown together with a detailed report of observations made on this accession.

elixir-fondue-datathon

ELIXIR FONDUE Datathon

gff2RDF

Convert the genome annotation of some crops into RDF

Marker2Sequence

Explore QTL regions for candidate genes.

MQ2

A simple python module to process output from MapQTL analysis.

MQ2_Web

A simple web interface for MQ2 to process output from MapQTL analysis.

pbr.github.com

Description Wageningen UR Plant Breeding github repository

PediHaplotyper

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

path2gene

CoSSA

Comparative Subsequence Sets Analysis (CoSSA) workflows to identify haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data

coreCollection

coreCollection

DeltaSNP

Extracting_knowledge_networks_from_literature-Scripts_for_Watson_potato

Scripts used for the work described in the manuscript

FAIR_CxE

Supporting information for the Manuscript: TITLE

flowerpowerparrot

script to download data of parrot flower power sensors using 'powerpot' API

GenesysParser

Client to read and parse accession (MCPD passport) information from GENESYS.

linked-data-demo

linked-data-demo_redirect

The redirection layer for the linked-data-demo project for plants.

ODEX-FAIRDataPoint

QTL-prioritisation

scripts

Random collection of scripts

SemGem

Semantic genebank integration

WatsonPotato

Additional material for the article: Extracting knowledge networks from plant scientific literature: Potato tuber flesh color as an exemplary trait.