ACT: aggregation and correlation toolbox for analyses of genome tracks

J Jee, J Rozowsky, KY Yip, L Lochovsky… - …, 2011 - academic.oup.com
J Jee, J Rozowsky, KY Yip, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang
Bioinformatics, 2011academic.oup.com
We have implemented aggregation and correlation toolbox (ACT), an efficient, multifaceted
toolbox for analyzing continuous signal and discrete region tracks from high-throughput
genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and
modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes
project. It is able to generate aggregate profiles of a given track around a set of specified
anchor points, such as transcription start sites. It is also able to correlate related tracks and …
Abstract
We have implemented aggregation and correlation toolbox (ACT), an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project. It is able to generate aggregate profiles of a given track around a set of specified anchor points, such as transcription start sites. It is also able to correlate related tracks and analyze them for saturation–i.e. how much of a certain feature is covered with each new succeeding experiment. The ACT site contains downloadable code in a variety of formats, interactive web servers (for use on small quantities of data), example datasets, documentation and a gallery of outputs. Here, we explain the components of the toolbox in more detail and apply them in various contexts.
Availability: ACT is available at http://act.gersteinlab.org
Contact:  [email protected]
Oxford University Press
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