Resources

AAGI-AU and its partners have developed a range of software tools and packages to help grains industry researchers with analysing and exploring their data.

R packages

  • biometryassist

    Functions to Assist Design and Analysis of Agronomic Experiments

    The biometryassist package provides user-friendly functions to aid in the design and analysis of agronomic and agricultural experiments.

    R CRAN package link

  • WGAIM

    Whole Genome Average Interval Mapping for QTL Detection and Estimation using ASReml-R

    WGAIM provides a computationally efficient whole genome approach to detecting and estimating significant QTL in linkage maps using the flexible linear mixed modelling functionality of ASReml-R.

    R CRAN package link

  • ASMap

    Linkage Map Construction using the MSTmap Algorithm

    ASMAP provides functions for accurate and fast linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred ‘R/qtl’ objects. This includes extremely fast linkage map clustering and optimal marker ordering using the MSTmap algorithm of Wu et al. (2008).

    R CRAN package link

  • nert

    Streamlined Access to the Australian TERN SMIPS Soil Moisture Datasets

    The nert package provides your R session with streamlined and user-friendly access to the Soil Moisture Integration and Prediction System (SMIPS) datasets generated by Australia’s Terrestrial Ecosystem Research Network (TERN). 

    GitHub repository link

  • lmmtools

    A Set of Tools for Linear Mixed Models

    The lmmtools package contains a variety of functions to augment the analysis of Linear Mixed Models fitted using ASReml-R.

    GitHub repository link

  • speed

    Generate Spatially Efficient Experimental Designs

    The speed package provides functions for generating spatially efficient designs for experiments, using model-free optimisation to rearrange treatments while maintaining statistical validity and design constraints.

    GitHub repository link

Bioinformatics tools

  • CoreDetector

    Fast and Flexible Multiple Genome Aligner Tool

    CoreDetector is a flexible and easy to use Java program for core-genome alignment, which can efficiently and accurately handle large and more evolutionary diverse genomes.

    GitHub repository link

  • HaploMaker

    Rapid Haplotype Assembly of Genomic Sequences

    HaploMaker is a reference-based haplotype assembly tool for diploid genomic sequences, which uses a novel and improved assembly algorithm for accurate and efficient phasing of longer haplotype regions.

    GitHub repository link

  • Comparative GO

    Webserver for Comparative Gene Ontology

    Comparative GO is a web application for comparative gene ontology, designed for researchers that want to study associations between gene ontology and list of genes or samples to understand biological pathways or select important genes for further analysis.

    Webserver homepage

GitHub

New and existing software tools are regularly developed and updated by the AAGI-AU team and its Strategic Partners and Project Partners. For the latest versions and developments, please see our associated GitHub organisation pages:

  • The AAGI-AUS GitHub contains a plethora of software tools and templates that have been developed by the AAGI Strategic Partners.
  • The Biometry Hub GitHub also contains many software packages developed by AAGI-AU’s software developers in the University of Adelaide’s Biometry Hub.