R and Bioconductor solutions for alternative splicing detection.
The detection of alternative splicing using microarray technology involves multiple computational steps: normalisation, filtering, detection and visualisation. In this review, these analyses are approached using the R and Bioconductor open-source computation solution. There is some discussion on how to integrate different Bioconductor packages, and some of their major features are demonstrated. In addition, the Xmap Genome Browser is incorporated as an integral part of the analysis and annotation workflow.
Phang
Tzulip
T
Department of Medicine, University of Colorado Denver School of Medicine, Denver, CO, USA. tzu.phang@ucdenver.edu
D000465:Algorithms; D017398:Alternative Splicing; D003628:Database Management Systems; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software