Computational Biology Group Software

To facilitate our research, we develop software to analyse data from various microarray 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
• BioHMM - R routine for the segmentation of aCGH that takes account of distances between clones along the genome (included in snapCGH)
• beadarray - R package for the analysis of Illumina BeadArray data

snapCGH: Segmentation, Normalisation And Processing of Array CGH data

We have developed an R package, snapCGH, for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.

After the data has been preprocessed and normalised, snapCGH allows the user to apply different segmentation schema available within R using a common style of input object. Additionally, we are developing a wide variety of functions in order to visualise the segmented data and to compare across multiple samples.

The following resources for snapCGH are available:

• practical for reading in and segmenting array CGH data: snapCGH practical I
• data for the first practical: snapCGH practical I data
• practical for comparing and visualising different aCGH segmentation results: snapCGH practical II
• data for the second practical: snapCGH practical II

The latest version of the package can be downloaded from Bioconductor.

beadarray: Analysis package for Illumina BeadArray data

We have developed an R package for the analysis of Illumina BeadArray data. The package is able to analyse data from both SAM (arrays arranged in 96-well plates) or BeadChip (6 / 8 samples on a chip) technologies. Data can be read into the package as bead summary data pre-processed by the Illumina BeadStudio software. Alternatively, full bead-level data can be read using TIFF images and positional information about each bead on an array.

Supplementary material for the beadarray package, including example data sets and instructions on how to change the scanner settings to obtain bead level data can be found at the Illumina Resources page.

The latest version of the package can be downloaded from Bioconductor.