USeq 7.7.5 Ranking & Summary
USeq 7.7.5 description
USeq 7.7.5 is such a professionally designed and user- friendly collection of software tool for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations. USeq is under continuous development at the Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.
A description of the statistics and comparison of methods used in USeq is now published, see Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. BMC Bioinformatics. 2008 Dec 5;9(1):523. Note, USeq now makes use of the DESeq R package to calculate p-values from a negative binomial distribution for differential enrichment/ reduction. See Anders S, Huber W: Differential expression analysis for sequence count data. Nature Precedings. 2010 Jan
- Java 1.6+
- R with Storey's Q-Value and Anders' DESeq libraries.
- Familiarity with command line programing
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