Software Developed In house

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 or Plotting Gene Ontology (ZIP 694.1KB) (The PloGO link points to a zip file) and Bioconductor Package


Software or Workflow

Tool / availability



  • SwathXtend Method of library merging and data analysis tool

Bioconductor package

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


  • Bioplex data normalization and analysis methodology

R Recipes

Breen et al, Scientific Reports 2016 and Cytokine 2015


  • TMTPrePro R package for analysis of TMT data

Internal tool

Mirzaei et al, Methods Mol Biol, to appear


  • Data analysis methodology and package

Internal tool

Pascovici et al, JPR 2015

Label Free

  • SCRAppy suite of scripts for analysis of label free data

Internal tool

Nielson et al, Methods Mol Biol 2013


  • PloGO R package for GO annotation and abundance plotting and enrichment analysis

Internal tool

Package available

Pascovici et al, Proteomics 2012

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
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