The Churchill Group develops software for statistical analysis of microarray experiments.

R/maanova provides a complete workflow for microarray analysis. It is implemented as an add-on package for the freely available and widely used statistical language/software R.

J/maanova is written in Java and, using R/maanova as the engine, provides a powerful and interactive working environment for users to perform a variety of tasks. A new release of this software is currently pending.

Churchill Group members within the Center for Genome Dynamics have developed several tools for systems level analysis including Genome Browser, Mouse Map Converter, Mouse Strain Comparison and Genome Interval Overlap Calculator.

Software for the analysis of Quantitative Trait Loci (QTL) data created by the Churchill Group.

R/qtl is developed by Karl W. Broman at the University of Wisconsin-Madison in collaboration with the Churchill Group. It is an extensible, interactive environment for QTL analysis. It is implemented as an add-on package for R language.

J/qtl is a Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl. It uses an intuitive point and click interface and is structured to guide an analyst through the appropriate sequence of steps.

Programs previously developed by the Churchill Group but no longer supported include Marker Regression Programs, PSEUDOMARKER, MANNOVA, Software to fit HIdden Markov Models.