signeR protocols

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signeR specifications

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Unique identifier OMICS_13434
Name signeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU Affero General Public License version 3
Computer skills Advanced
Version 1.6.1
Stability Stable
Requirements
methods, stats, graphics, BiocGenerics, GenomicRanges, utils, Biostrings, rtracklayer, grDevices, BSgenome.Hsapiens.UCSC.hg19, knitr, class, VariantAnnotation, nloptr, NMF, PMCMR
Maintained Yes

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Maintainer


  • person_outline Renan Valieris <>

Publication for signeR

signeR in pipeline

2017
PMCID: 5501799
PMID: 28687745
DOI: 10.1038/s41598-017-04743-0

[…] each gene separately. gene snv counts were then hierarchically clustered using the heatmap.2 function of the gplots r package. mutation signatures were calculated and visualized using the r package signer (version 1.0.1)., rna-seq data and clinical data from the paad tcga dataset were obtained from https://genome-cancer.ucsc.edu/ (supplemental material ). overall, data from 163 patients […]

signeR institution(s)
Departamento de Computação e Matemática, Universidade de São Paulo, São Paulo, Brazil; Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo, Brazil; Laboratory of Medical Genomics, A. C. Camargo Cancer Center, São Paulo, Brazil; Laboratory of Neurosciences (LIM27), Department and Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil; Laboratory of Molecular Immunology, The Rockefeller University, NY, USA
signeR funding source(s)
This work was partially supported by Fundação de Apoio a Pesquisa do Estado de São Paulo, grant 15/19324-6.

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