ACT: aggregation and correlation toolbox for analyses of genome tracks
| Autor: | Yutao Fu, Kevin Y. Yip, Robert D. Bjornson, Zhengdong D. Zhang, Justin Jee, Joel Rozowsky, Jie Wang, Zhiping Weng, Mark Gerstein, Guoneng Zhong, Lucas Lochovsky |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Statistics and Probability
Web server Computer science Genomics Single-nucleotide polymorphism ENCODE computer.software_genre Polymorphism Single Nucleotide Biochemistry Genome Set (abstract data type) Software 1000 Genomes Project Molecular Biology business.industry SIGNAL (programming language) Genome Analysis Toolbox Computer Science Applications Applications Note Computational Mathematics Computational Theory and Mathematics Data mining Transcription Initiation Site business computer |
| Zdroj: | Bioinformatics |
| ISSN: | 1460-2059 1367-4803 |
| DOI: | 10.1093/bioinformatics/btr092 |
| Popis: | 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: gro.balnietsreg@ip |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|