Rat on Genome Sequenceer Courtesy of Martin Krzywinski  

RATb: Report and Analysis Template Builder, Part 1/2

Select one template from each section. Then press the 'Submit' button at the bottom of the page.

Header Templates

universalHead.Rnw This Rnw file contains the standard prefix for all reports. This includes the \documentclass and \begin{document} commands. It sets up some standard defintions and options, creates a subdirectory to store figures, and lays out the required Executive Summary section. The point of including a structured Executive Summary (or extended abstract) is to make it easier for biologists to interpret reports.
minimalHead.Rnw This Rnw file contains a minimal LaTeX header. This includes the \documentclass and \begin{document} commands, and almost nothing else. You really do not want to use this header; it only exists to test some of the capabilities of the Report Template Builder.

Main Processing Templates

Preprocessing or Quality Control

doNothing.Rnw This minimal Rnw file contains no LaTeX markup. You probably only want to use this file in order to take advantage of the standard layout produced by the headers and trailers.
bundle.Rnw Most of our analysis routines assume that their input comes from binary Rdata files containng a numeric data matrix and a sample information data frame. While our platform-specific QC processing scripts produce these kinds of files, it is often useful to start directly from analogous data sources. This script bundles two tab-separated-values (TSV) files together into an Rdata file.
affyProcessQC.Rnw This Rnw file contains code to process a standard (small) Affymetrix gene expression dataset, including a suite of quality control (QC) measures.
agilentExpression.Rnw This Rnw file contains code to process a standard (small) Agilent 44K gene expression dataset, including a suite of quality control (QC) measures.
lumiExpression.Rnw This Rnw file contains code to process a standard (small) Illumina gene expression dataset, including a suite of quality control (QC) measures.
ExiqonMicroRNA.Rnw This Rnw file contains code to process a Exiqon microRNA dataset, including a suite of quality control (QC) measures.
rppaProcess.Rnw This Rnw file contains code to process a rppa dataset.

Analysis

twoGroups.Rnw This Rnw file contains code to perform a simple two-group comparison, with corrections for multiple testing based on the false discovery rate (FDR) as estimated by a beta-uniform mixture (BUM) model.
unsupervised.Rnw This Rnw file contains an unsupervised analysis looking for sample clusters in a high-thoughput dataset.
onewayAnova.Rnw This Rnw file contains code to perform a simple comparison for multiple groups (more than two), with corrections for multiple testing based on the false discovery rate (FDR) as estimated by a beta-uniform mixture (BUM) model.

Trailer Templates

universalTail.Rnw This Rnw file contains the standard appendix, which displays the current working directory and the R session information. It concludes with an \end{document} command.
minimalTail.Rnw This Rnw file contains the shortest possible trailer: an \end{document} command. You almost certainly do not want to use this trailer.