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The course participants will learn how to use BioConductor software and Illumina BaseSpace Cloud apps. In the first three days, the course covers various topics using the oneChannelGUI graphical interface. The last day is dedicated to providing the basics to move from the use of the graphical environment to command line. The basics of R scripting will be described and some of the workflows used in the first three days will be dissected and executed using command line approach. All computers for hands-on exercises will be provided along with demo data sets.