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Popular tool citations

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SigFuge specifications

Information


Unique identifier OMICS_05201
Name SigFuge
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data data matrix of coverage
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.18.0
Stability Stable
Requirements
GenomicRanges, BiocStyle, ggplot2, org.Hs.eg.db, R(>=3.1.1), reshape, TxDb.Hsapiens.UCSC.hg19.knownGene, matlab, sigclust, prebsdata, Rsamtools(>=1.17.0)
Maintained Yes

Versioning


No version available

Documentation


Publication for SigFuge

SigFuge citation

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Transcriptome sequencing reveals altered long intergenic non coding RNAs in lung cancer

2014
Genome Biol
PMCID: 4156652
PMID: 25116943
DOI: 10.1186/s13059-014-0429-8

[…] by counting the read depth at each base using custom perl scripts and the bio::db::sam bioperl package. coverage maps shown in figure and in figure s5 in additional file were created in r using sigfuge version 1.1.2 []. for the tables shown in figure and in figure s5 in additional file , the cutoff for classifying samples as high or low expression was determined by maximizing the matthews […]


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SigFuge institution(s)
Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Genome Institute, Washington University School of Medicine, St Louis, MO, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Multidisciplinary Thoracic Oncology Program, Division of Medical Oncology, Department of Internal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

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