Software Developed In house
Bioinformatics tools we have developed in house to address specific data analysis or reporting needs. The packages themselves are open source and freely available; internally they can be accessed via a graphical user interface provided by a local GenePattern server. The tools available can be found at http://bio.proteome.org.au or Plotting Gene Ontology (ZIP 694.1KB) (The PloGO link points to a zip file) and Bioconductor Package
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Technique
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Software or Workflow
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Tool / availability
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Publication
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SWATH
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- SwathXtend Method of library merging and data analysis tool
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Bioconductor package
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Wu et al, MCP 2016; SwathXtend library merging module takes a seed library and one or more add-on libraries and generating an extended assay library ready to be used for SWATH extraction
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BioPlex
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- Bioplex data normalization and analysis methodology
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R Recipes
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Breen et al, Scientific Reports 2016 and Cytokine 2015
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TMT
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- TMTPrePro R package for analysis of TMT data
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Internal tool
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Mirzaei et al, Methods Mol Biol, to appear
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iTRAQ
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- Data analysis methodology and package
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Internal tool
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Pascovici et al, JPR 2015
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Label Free
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- SCRAppy suite of scripts for analysis of label free data
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Internal tool
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Nielson et al, Methods Mol Biol 2013
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GO
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- PloGO R package for GO annotation and abundance plotting and enrichment analysis
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Internal tool
Package available
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Pascovici et al, Proteomics 2012
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Areas of expertise/strength
- Statistical and machine-learning based data analysis of a wide variety of novel proteomic techniques (SWATH, immunoassays, protein arrays, labelled isobaric, label free)
- Data analysis capability in areas such as GLM, hierarchical designs, linear and mixed models, classification, machine learning and statistical significance analysis
- Experiment design for proteomics, block design
- Screening for cytokine, chemokines, interleukins and hormones for high through put diagnostics and clinical analysis with in-depth Bio-Plex® analysis
- Agricultural plant proteomics with an emphasis on stress responses to drought, disease or pathogens
- Deriving insights from close collaborations with biologists, analytical chemists, clinicians and various other researchers