Package: genefu 2.39.1

Benjamin Haibe-Kains

genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

Authors:Deena M.A. Gendoo [aut], Natchar Ratanasirigulchai [aut], Markus S. Schroeder [aut], Laia Pare [aut], Joel S Parker [aut], Aleix Prat [aut], Nikta Feizi [ctb], Christopher Eeles [ctb], Jermiah Joseph [ctb], Benjamin Haibe-Kains [aut, cre]

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NEWS

# Install 'genefu' in R:
install.packages('genefu', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • annot.expos - Gene expression, annotations and clinical data from the International Genomics Consortium
  • annot.nkis - Gene expression, annotations and clinical data from van de Vijver et al. 2002
  • annot.vdxs - Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
  • claudinLowData - ClaudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.
  • data.expos - Gene expression, annotations and clinical data from the International Genomics Consortium
  • data.nkis - Gene expression, annotations and clinical data from van de Vijver et al. 2002
  • data.vdxs - Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
  • demo.expos - Gene expression, annotations and clinical data from the International Genomics Consortium
  • demo.nkis - Gene expression, annotations and clinical data from van de Vijver et al. 2002
  • demo.vdxs - Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
  • mod1 - Gene modules published in Desmedt et al. 2008
  • mod2 - Gene modules published in Wirapati et al. 2008
  • modelOvcAngiogenic - Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.
  • pam50 - PAM50 classifier for identification of breast cancer molecular subtypes
  • pam50.robust - PAM50 classifier for identification of breast cancer molecular subtypes
  • pam50.scale - PAM50 classifier for identification of breast cancer molecular subtypes
  • scmgene.robust - Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes
  • scmod1.robust - Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes
  • scmod2.robust - Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes
  • sig.endoPredict - Signature used to compute the endoPredict signature as published by Filipits et al 2011
  • sig.gene70 - Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002
  • sig.gene76 - Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005
  • sig.genius - Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.
  • sig.ggi - Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006
  • sig.oncotypedx - Signature used to compute the OncotypeDX signature as published by Paik et al 2004
  • sig.pik3cags - Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006
  • sig.tamr13 - Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.
  • sigOvcAngiogenic - SigOvcAngiogenic dataset
  • sigOvcCrijns - SigOvcCrijns dataset
  • sigOvcSpentzos - SigOcvSpentzos dataset
  • sigOvcTCGA - SigOvcTCGA dataset
  • sigOvcYoshihara - SigOvcYoshihara dataset
  • ssp2003 - SSP2003 classifier for identification of breast cancer molecular subtypes
  • ssp2003.robust - SSP2003 classifier for identification of breast cancer molecular subtypes
  • ssp2003.scale - SSP2003 classifier for identification of breast cancer molecular subtypes
  • ssp2006 - SSP2006 classifier for identification of breast cancer molecular subtypes
  • ssp2006.robust - SSP2006 classifier for identification of breast cancer molecular subtypes
  • ssp2006.scale - SSP2006 classifier for identification of breast cancer molecular subtypes

On BioConductor:genefu-2.39.0(bioc 3.21)genefu-2.37.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialexpressiongeneexpressionvisualizationclusteringclassification

7.41 score 3 packages 191 scripts 645 downloads 42 mentions 50 exports 103 dependencies

Last updated 25 days agofrom:1ef27ec808. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 28 2024
R-4.5-winWARNINGNov 28 2024
R-4.5-linuxWARNINGNov 28 2024
R-4.4-winWARNINGNov 28 2024
R-4.4-macWARNINGNov 28 2024
R-4.3-winWARNINGNov 28 2024
R-4.3-macWARNINGNov 28 2024

Exports:bimodboxplotplus2claudinLowcollapseIDscompareProtoCorcompute.pairw.cor.metacompute.pairw.cor.zcompute.proto.cor.metacordiff.dependoPredictfuzzy.ttestgene70gene76geneid.mapgeniusggiihc4intrinsic.clusterintrinsic.cluster.predictmap.datasetsmedianCtrmolecular.subtypingnpioncotypedxovcAngiogenicovcCrijnsovcTCGAovcYoshiharaoverlapSetspik3cagspower.corps.clusterread.m.filereadArrayrename.duplicaterescalerorSsetcolclass.dfsig.scorespearmanCIst.gallenstab.fsstab.fs.rankingstrescRsubtype.clustersubtype.cluster.predicttamr13tbrmweighted.meanvarwrite.m.file

Dependencies:AIMSamapAnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootstrapcachemclasscliclustercodetoolscpp11crayoncurldata.tableDBIdbplyrdiagramdigestdplyre1071fansifastmapfilelockfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataglobalsgluehmshttrhttr2iC10iC10TrainingDataimputeipredIRangesjsonliteKEGGRESTKernSmoothlatticelavalifecyclelimmalistenvmagrittrMASSMatrixmclustmemoisemimennetnumDerivopensslpamrparallellypillarpkgconfigplogrpngprettyunitsprodlimprogressprogressrproxypurrrR6rappdirsRcpprlangrmetarpartRSQLiteS4VectorsshapeSQUAREMstatmodstringistringrSuppDistssurvcompsurvivalsurvivalROCsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc

genefu: A Package for Breast Cancer Gene Expression Analysis

Deena M.A. Gendoo, Natchar Ratanasirigulchai, Markus Schröder, Laia Pare, Joel S.Parker - &nc Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC27599, USA, Aleix Prat, Benjamin Haibe-Kains

Rendered fromgenefu.Rmdusingknitr::rmarkdownon Nov 28 2024.

Last update: 2021-05-21
Started: 2021-01-12

Readme and manuals

Help Manual

Help pageTopics
Function to identify bimodality for gene expression or signature scorebimod
Box plot of group of values with corresponding jittered pointsboxplotplus2
Claudin-low classification for Breast Cancer DataclaudinLow
claudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.claudinLowData
Utility function to collapse IDscollapseIDs
Function to statistically compare correlation to prototypescompareProtoCor
Function to compute pairwise correlations in a meta-analytical frameworkcompute.pairw.cor.meta
Function to compute the Z transformation of the pairwise correlations for a list of datasetscompute.pairw.cor.z
Function to compute correlations to prototypes in a meta-analytical frameworkcompute.proto.cor.meta
Function to estimate whether two dependent correlations differcordiff.dep
Function to compute the endoPredict signature as published by Filipits et al 2011endoPredict
Gene expression, annotations and clinical data from the International Genomics Consortiumannot.expos data.expos demo.expos expos
Function to compute the fuzzy Student t test based on weighted mean and weighted variancefuzzy.ttest
Function to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002gene70
Function to compute the Relapse Score as published by Wang et al. 2005gene76
Function to find the common genes between two datasets or a dataset and a gene listgeneid.map
Function to compute the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010genius
Function to compute the raw and scaled Gene expression Grade Index (GGI)ggi
Function to compute the IHC4 prognostic score as published by Paik et al. in 2004.ihc4
Function to fit a Single Sample Predictor (SSP) as in Perou, Sorlie, Hu, and Parker publicationsintrinsic.cluster
Function to identify breast cancer molecular subtypes using the Single Sample Predictor (SSP)intrinsic.cluster.predict
Function to map a list of datasets through EntrezGene IDs in order to get the union of the genesmap.datasets
Center around the medianmedianCtr
Gene modules published in Desmedt et al. 2008mod1
Gene modules published in Wirapati et al. 2008mod2
Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.modelOvcAngiogenic
Function to identify breast cancer molecular subtypes using the Subtype Clustering Modelmolecular.subtyping
Gene expression, annotations and clinical data from van de Vijver et al. 2002annot.nkis data.nkis demo.nkis nkis
Function to compute the Nottingham Prognostic Indexnpi
Function to compute the OncotypeDX signature as published by Paik et al. in 2004.oncotypedx
Function to compute the subtype scores and risk classifications for the angiogenic molecular subtype in ovarian cancerovcAngiogenic
Function to compute the subtype scores and risk classifications for the prognostic signature published by Crinjs et al.ovcCrijns
Function to compute the prediction scores and risk classifications for the ovarian cancer TCGA signatureovcTCGA
Function to compute the subtype scores and risk classifications for the prognostic signature published by Yoshihara et al.ovcYoshihara
Overlap two datasetsoverlapSets
PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)pam50 pam50.robust pam50.scale
Function to compute the PIK3CA gene signature (PIK3CA-GS)pik3cags
Function for sample size calculation for correlation coefficientspower.cor
Function to compute the prediction strength of a clustering modelps.cluster
Function to read a 'csv' file containing gene lists (aka gene signatures)read.m.file
Overlap two datasetsreadArray
Function to rename duplicated stringsrename.duplicate
Function to rescale values based on quantilesrescale
Function to compute the rorS signature as published by Parker et al 2009rorS
Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypesscmgene.robust
Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)scmod1.robust
Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)scmod2.robust
Function to set the class of columns in a data.framesetcolclass.df
Signature used to compute the endoPredict signature as published by Filipits et al 2011sig.endoPredict
Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002sig.gene70
Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005sig.gene76
Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.sig.genius
Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006sig.ggi
Signature used to compute the OncotypeDX signature as published by Paik et al 2004sig.oncotypedx
Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006sig.pik3cags
Function to compute signature scores as linear combination of gene expressionssig.score
Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.sig.tamr13
sigOvcAngiogenic datasetsigOvcAngiogenic
sigOvcCrijns datasetsigOvcCrijns
sigOcvSpentzos datasetsigOvcSpentzos
sigOvcTCGA datasetsigOvcTCGA
sigOvcYoshihara datasetsigOvcYoshihara
Function to compute the confidence interval for the Spearman correelation coefficientspearmanCI
SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)ssp2003 ssp2003.robust ssp2003.scale
SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)ssp2006 ssp2006.robust ssp2006.scale
Function to compute the St Gallen consensus criterion for prognosticationst.gallen
Function to quantify stability of feature selectionstab.fs
Function to quantify stability of feature rankingstab.fs.ranking
Utility function to escape LaTeX special characters present in a stringstrescR
Function to fit the Subtype Clustering Modelsubtype.cluster
Function to identify breast cancer molecular subtypes using the Subtype Clustering Modelsubtype.cluster.predict
Function to compute the risk scores of the tamoxifen resistance signature (TAMR13)tamr13
Function to compute Tukey's Biweight Robust Meantbrm
Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007annot.vdxs data.vdxs demo.vdxs vdxs
Function to compute the weighted mean and weighted variance of 'x'weighted.meanvar
Function to write a 'csv' file containing gene lists (aka gene signatures)write.m.file