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REEF specifications

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Unique identifier OMICS_19618
Name REEF
Alternative name REgionally Enriched Features
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Medium
Stability No
Requirements
python interpreter, wxPython GUI toolkit
Source code URL http://www.biomedcentral.com/content/supplementary/1471-2105-7-453-S1.tgz
Maintained No

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Publication for REgionally Enriched Features

REEF citations

 (3)
library_books

Systems biological approaches towards understanding cellulase production by Trichoderma reesei

2013
J Biotechnol
PMCID: 3568919
PMID: 22750088
DOI: 10.1016/j.jbiotec.2012.05.020

[…] to 275 kb in length at an average density of fivefold greater than the expected density for randomly distributed genes. since these data were only manually obtained, we reassessed this with reef (“regionally enriched features”), a software that identifies genomic regions enriched in specific features using a statistic test based on the hypergeometric distribution by using a sliding window […]

library_books

Comparative gene expression profiling between human cultured myotubes and skeletal muscle tissue

2010
BMC Genomics
PMCID: 2838843
PMID: 20175888
DOI: 10.1186/1471-2164-11-125

[…] ipa canonical pathways are well-characterized metabolic and cell-signaling pathways coming from articles, reviews, books, and kegg ligand., gene cluster analysis was performed with the reef (regionally enriched features in genomes) program, which scans the genome using a sliding window approach, and calculates the statistical significance of each window using the hypergeometric […]

library_books

Genomic expression during human myelopoiesis

2007
BMC Genomics
PMCID: 2045681
PMID: 17683550
DOI: 10.1186/1471-2164-8-264

[…] development, muscle development and function, nervous system development, skeletal development, spermatogenesis, visual perception., for each non-hematopoietic module we identified, by using reef (regionally enriched features) [], positional enrichment of module-related genes (sliding window = 1 mb; window shift = 200 kb; q-value cut-off = 0.05; min number of genes in cluster = 2) (additional […]


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REEF institution(s)
Department of Biology, University of Padova, Padova, Italy
REEF funding source(s)
Supported by the University of Padova and of the Italian Ministry of University and Scientific and Technological Development, UCSC Genome Browser and GeneAnnot.

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