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Short description:
Please summarise the application in a few sentences. Avoid links here. 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
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
ChIP-on-chip, ChIP-seq, DNA packaging, Epigenomics
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Annotation, Peak calling
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina, 454, SOLiD, Ion Torrent, Illumina HiSeq,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Molecular Modelling & Bioinformatics Unit. Joint programme IRB-BSC & University of Barcelona
== 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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