Quantitative Enrichment of Sequence Tags: QuEST
QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).
QuEST 2.4 is available. See link on the right.
New in 2.4:
Filtering of outlier regions based on control data
New in 2.3:
Use of fold-enrichment to normalize for the depth of sequencing, size of the genome, and expectation of tag distribution under uniformity. This makes selection of peak calling parameters more intuitive and results in more interpretable ChIP enrichment scores. Underlying algorithms have not changed over 2.2.
Improved in 2.2:
New features in 2.0:
NOTE: we do not make precompiled versions available because of the large number of computational platforms we would have to support. You can compile QuEST easily if you have a standard installation of the gnu C compiler, which comes with most Linux systems. Mac users need to install the Developer Tools package (which comes with every system install disk but does not get installed by default). After you install Developer Tools, the C compiler will be in /usr/bin/gcc and the system will know where to find it.
Original QuEST Paper
QuEST data from the paper (BIG FILES)
Funded by NIH/NHGRI and by the Stanford Pathology/Genetics UHTS Initiative