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Software developed by the Statistics and Computational Biology Group

To facilitate our research, we develop software to analyse data from various microarray and sequencing platforms. This software is mainly written in the R statistical programming language and is made available as part of the Bioconductor project. Our software includes:

  • snapCGH - R package for the analysis of aCGH
    includes BioHMM - R routine for the segmentation of aCGH that takes account of distances between clones along the genome
  • beadarray - R package for the analysis of Illumina BeadArray data
  • IDATreader - An R package for the reading of encrypted Illumina expression array idat files
  • CNAseg - method for identification of copy number changes in cancer from second-generation sequencing data
  • CNAnova - statistical framework for identifying recurrent regions of copy number changes
  • BayesPeakA Bioconductor package for peak-calling in ChIP-seq data.
  • Sparse Partitioning - tool for identifying interactions in medium / high dimension regression problems
  • multiSNV - tool for calling somatic SNVs from multiple samples of the same patient
  • IONiseR - An R package for quality assessment of Oxford Nanopore MinION data