F-Seq

F-Seq: a feature density estimator for high-throughput sequence tags. Summary: Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display individual sequence data as an accurate and interpretable signal, we developed F-Seq, a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser. Availability: The software is written in the Java language and is available on all major computing platforms for download at http://www.genome.duke.edu/labs/furey/software/fseq.


References in zbMATH (referenced in 5 articles )

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  1. Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)
  2. Ding, Min; Wang, Haiyun; Chen, Jiajia; Shen, Bairong; Xu, Zhonghua: Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data (2012)
  3. Humburg, Peter; Helliwell, Chris A.; Bulger, David; Stone, Glenn: Chipseqr: analysis of chip-seq experiments (2011) ioport
  4. Li, Qunhua; Brown, James B.; Huang, Haiyan; Bickel, Peter J.: Measuring reproducibility of high-throughput experiments (2011)
  5. Boyle, Alan P.; Guinney, Justin; Crawford, Gregory E.; Furey, Terrence S.: F-seq: a feature density estimator for high-throughput sequence tags. (2008) ioport