RATb: The Report and Analysis Template Builder

The Report and Analysis Template Builder (RATb) uses XML and R to create reusable, structured Sweave files for the statistical and bioinformatic analysis of high-throughput 'omics' datasets.

Auxuliary material

Some templates refer to auxiliary data or information; those are stored at ./Auxiliary


The XML component is used to describe the replacable parameters in a template file; the data in these files drives the construction of the RATb web site. The XML DTD file is really quite simple. It defines the 'Templates' document type to be a list of one or more 'Template' objects. Each 'Template' consists of:

  • a 'FileName', which is the location of the actual source of the template,
  • a 'Description', which is a short paragraph explaining the purpose of the template, and
  • a set of 'Parameters'.
In turn, the 'Parameters' form a list of 'Item' objects. The 'Name' of an 'Item' is the name of the parameter in the template file. The contents of an 'Item' describes the semantics/interpretation of that parameter. Optionally, a parameter 'Item' can have a 'Default' value, and a yes/no indicator of whether it is 'Long' (and so needs an entire text area in a form) or not (and so can fit into a smaller text field).

The actual template files are prepared as Sweave files. Sweave is a tool that combines the R statistical programming environment with the LaTeX typesetting system. This combination provides a powerful tool for conducting reproducible research.

Template files should be categorized (in the 'Type' attribute of the XML 'Template' entry) as one of four types: 'header', 'trailer', 'qc', or 'analysis'. (In our templates, preprocessing steps are included under 'qc'.) The types are used to organize the layout on the web site. A complete filled-in template file consists of one header, one processor that is either 'qc' or 'analysis', and one 'trailer'. Thus, most of the actual analysis templates are constructed without LaTex preambles or \begin{document} or \end{document} commands.

If you would like to contribute a template to the RATb project, please contact Kevin Coombes at the M.D. Anderson Cancer Center.