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Application data |
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| Created by | Flores O, Orozco M |
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| Biological application domain(s) | ChIP-Chip, ChIP-Seq, Nucleosome Positioning, Epigenomics |
| Principal bioinformatics method(s) | Annotation, Peak calling, Protein Binding Peak Detection, Peak detection, Peak finding, Programming Library |
| Technology | any |
| Created at | Molecular Modelling & Bioinformatics Unit. Joint programme IRB-BSC & University of Barcelona |
| Maintained? | Yes |
| Input format(s) | ShortRead, Other formats supported by BioConductor |
| Output format(s) | WIG, BED, Other formats supported by BioConductor |
| Software features | Multicore, Integrated solution |
| Programming language(s) | R |
| Licence | LGPL3 |
| Operating system(s) | Cross-Platform |
Summary: nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling
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Description
We present a new tool, nucleR, integrated in the open source, multiplatform R/Bioconductor framework. The approach is based on a fast, non-parametric detection of all nucleosome dyads and scoring of the calls. A good performance is achieved by filtering the noise using Fast Fourier Transform (FFT). The user has full freedom to export, select, merge or process suggested nucleosome calls in any desired way, making the method completely flexible. Algorithms presented here are suitable for most Tiling Arrays and single or paired ended Next Generation Sequencing platforms
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