Genefu protocols

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Genefu specifications


Unique identifier OMICS_11530
Name Genefu
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.12.0
Stability Stable
limma, amap, R(>=2.10), biomaRt, mclust, survcomp, iC10, AIMS
Maintained Yes



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  • person_outline Benjamin Haibe-Kains <>

Publications for Genefu

Genefu in pipelines

PMCID: 5550415
PMID: 28794488
DOI: 10.1038/s41467-017-00244-w

[…] signature (pam50) to classify single cells and nuclei into five established intrinsic breast cancer molecular subtypes (normal-like, basal, luminal a, luminal b, and her2 amplification) using “genefu” package with log2(tpm + 1) data matrix. single cells or nuclei with low prediction confidence (<0.7) are set as undefined. in a separate analysis, single nuclei were classified into six […]

PMCID: 5308655
PMID: 27665539
DOI: 10.18632/oncotarget.11038

[…] spia v2.22.0, []) as described before []. samples were stratified according to the subgroups proposed by tothill et al. [], the tcga [], and in angiogenic and non-angiogenic [] using the r-package genefu v2.2.0 ( these subgroups were compared to the proposed tumor spread types miliary and non-miliary corrected for tumor tissue origin (p, m, a, […]

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Genefu in publications

PMCID: 5940770
PMID: 29739984
DOI: 10.1038/s41598-018-25357-0

[…] the same number of er+ tumors randomly drawn from tcga. log2 transcripts per million (tpm) of all tumors were then median centered by extracting the median calculated from er balanced sub-samples. genefu r package was used to assign intrinsic subtypes for all tumors using median centered data. we repeated drawing er balanced samples 100 times, and the most frequently assigned subtypes were use […]

PMCID: 5928087
PMID: 29713003
DOI: 10.1038/s41467-018-04129-4

[…] intrinsic subtypes—ihc, pam50, and nmc. the ihc subtypes were determined by ihc assays for er, pr, and her2 and used in clinical diagnoses and treatment. pam50 subtypes were predicted using genefu from the gene expression data. we developed an in-house breast cancer subtype classifier called naïve molecular classifier (nmc) based on erbb2, esr1, and pgr gene expression and erbb2 copy […]

PMCID: 5921990
PMID: 29699511
DOI: 10.1186/s12885-018-4388-4

[…] from log-rank test in kaplan-meier analysis were used to represent the statistical significance of differential survival probabilities between different patient groups. we used bioconductor genefu package [] to compare the ymr signature developed from the common signature genes with other prognostic signatures including our previous ymr-16, mammaprint, oncotypedx and multigene […]

PMCID: 5875760
PMID: 29596496
DOI: 10.1371/journal.pone.0193871

[…] genes for normalization) to estimate a continuous score truncated to ranges from 0 to 100 for low to high risk respectively, three risk categories are assigned accordingly []. we used the r-package genefu [] to estimate the continuous non-truncated recurrence score and risk category from microarray data and avoid additional non-linearities produced by the truncation process. as suggested […]

PMCID: 5844884
PMID: 29523784
DOI: 10.1038/s41467-018-03264-2

[…] breast cancer molecular subtypes have been assigned using the pam50 intrinsic subtype classifier, i.e., the intrinsic.cluster.predict function, of the genefu r package. gene expression heatmaps have been generated using the function heatmap.2 of r gplots package after row-wise standardization of the expression values. average signature expression […]

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Genefu institution(s)
Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, UK; Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA; Translational Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain; Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
Genefu funding source(s)
A CIBC-Brain Canada Brain Cancer Research Training Award; the Gattuso Slaight Personalized Cancer Medicine Fund; Cancer Research Society; CIHR Grant 201412MSH-340176-229599; the Instituto de Salud Carlos III -PI13/01718; a Career Catalyst Grant from the Susan Komen Foundation; Banco Bilbao Vizcaya Argentaria (BBVA) Foundation

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