The first public release of Cufflinks is now available for download. Cufflinks is a toolkit for analyzing single cell expression experiments. It runs on the R statistical computing platform. Cufflinks takes as input a matrix of gene or transcript expression values, along with information about each cell in the experiment, and some annotation about each gene/transcript, both provided as simple tables. It is designed for single-cell RNA-Seq experiments, but in principle Cufflinks can be used with other data types such as qPCR. For RNA-Seq, you can use Cufflinks to estimate your expression values. This software is a work in progress - it is a beta release, and new features will continue to be added over the next couple of weeks. To suggest a feature or report a bug, please post your comments on the Cufflinks user’s group.