ACT: aggregation and correlation toolbox for analyses of genome tracks
Yip, Kevin Y.
Gerstein, Mark B.
UMass Chan AffiliationsProgram in Bioinformatics and Integrative Biology
Department of Biochemistry and Molecular Pharmacology
Polymorphism, Single Nucleotide
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AbstractWe 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: firstname.lastname@example.org.
SourceBioinformatics. 2011 Apr 15;27(8):1152-4. doi: 10.1093/bioinformatics/btr092. Link to article on publisher's site
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/25884
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Rights© The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.