Course material

• Lecture
• Exercises

Data

• Data for the exercises

Literature

• Primer on clustering
• Primer on principal component analysis
• Primer on motifs
• Primer on motif discovery
• Evening element paper on the circadian clock in Arabidopsis

Packages and related R documents

• The package ClassDiscovery used in the exercises is not part of Bioconductor and can be downloaded here
• Open source cluster programs
  • XCluster
  • Cluster ( + TreeView and Maple Tree)
• The ctc package from Bioconductor provides functions for communication with these programs
• The amap package from CRAN offers optimized functions for clustering large datasets

• Another useful tool for clustering is TIGR Multiexperiment Viewer (TMEV). TMEV is also installed on the PCs in the exercise rooms