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

Description: 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.

AuthorDeena M.A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, Joel S. Parker, Aleix Prat, and Benjamin Haibe-Kains
Date of publicationNone
MaintainerBenjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>, Markus Schroeder <markus.schroeder@ucdconnect.ie>
LicenseArtistic-2.0
Version2.6.0
http://www.pmgenomics.ca/bhklab/software/genefu

View on Bioconductor

Man pages

bimod: Function to identify bimodality for gene expression or...

boxplotplus2: Box plot of group of values with corresponding jittered...

claudinLow: Claudin-low classification for Breast Cancer Data

claudinLowData: claudinLowData for use in the claudinLow classifier. Data...

collapseIDs: Utility function to collapse IDs

compare.proto.cor: Function to statistically compare correlation to prototypes

compute.pairw.cor.meta: Function to compute pairwise correlations in a...

compute.pairw.cor.z: Function to compute the Z transformation of the pairwise...

compute.proto.cor.meta: Function to compute correlations to prototypes in a...

cordiff.dep: Function to estimate whether two dependent correlations...

endoPredict: Function to compute the endoPredict signature as published by...

expos: Gene expression, annotations and clinical data from the...

fuzzy.ttest: Function to compute the fuzzy Student t test based on...

gene70: Function to compute the 70 genes prognosis profile (GENE70)...

gene76: Function to compute the Relapse Score as published by Wang et...

genefu-package: Relevant Functions for Gene Expression Analysis, Especially...

geneid.map: Function to find the common genes between two datasets or a...

genius: Function to compute the Gene Expression progNostic Index...

ggi: Function to compute the raw and scaled Gene expression Grade...

ihc4: Function to compute the IHC4 prognostic score as published by...

intrinsic.cluster: Function to fit a Single Sample Predictor (SSP) as in Perou,...

intrinsic.cluster.predict: Function to identify breast cancer molecular subtypes using...

map.datasets: Function to map a list of datasets through EntrezGene IDs in...

medianCtr: Center around the median

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...

molecular.subtyping: Function to identify breast cancer molecular subtypes using...

nkis: Gene expression, annotations and clinical data from van de...

npi: Function to compute the Nottingham Prognostic Index

oncotypedx: Function to compute the OncotypeDX signature as published by...

ovcAngiogenic: Function to compute the subtype scores and risk...

ovcCrijns: Function to compute the subtype scores and risk...

ovcTCGA: Function to compute the prediction scores and risk...

ovcYoshihara: Function to compute the subtype scores and risk...

overlapSets: Overlap two datasets

pam50: PAM50 classifier for identification of breast cancer...

pik3cags: Function to compute the PIK3CA gene signature (PIK3CA-GS)

power.cor: Function for sample size calculation for correlation...

ps.cluster: Function to compute the prediction strength of a clustering...

readArray: Overlap two datasets

read.m.file: Function to read a 'csv' file containing gene lists (aka gene...

rename.duplicate: Function to rename duplicated strings.

rescale: Function to rescale values based on quantiles

rorS: Function to compute the rorS signature as published by Parker...

scmgene.robust: Subtype Clustering Model using only ESR1, ERBB2 and AURKA...

scmod1.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...

scmod2.robust: Subtype Clustering Model using ESR1, ERBB2 and AURKA modules...

setcolclass.df: Function to set the class of columns in a data.frame

sig.endoPredict: Signature used to compute the endoPredict signature as...

sig.gene70: Signature used to compute the 70 genes prognosis profile...

sig.gene76: Signature used to compute the Relapse Score (GENE76) as...

sig.genius: Gene Expression progNostic Index Using Subtypes (GENIUS) as...

sig.ggi: Gene expression Grade Index (GGI) as published in Sotiriou et...

sig.oncotypedx: Signature used to compute the OncotypeDX signature as...

sigOvcAngiogenic: a

sigOvcCrijns: a

sigOvcSpentzos: a

sigOvcTCGA: a

sigOvcYoshihara: a

sig.pik3cags: Gene expression Grade Index (GGI) as published in Sotiriou et...

sig.score: Function to compute signature scores as linear combination of...

sig.tamr13: Tamoxifen Resistance signature composed of 13 gene clusters...

spearmanCI: Function to compute the confidence interval for the Spearman...

ssp2003: SSP2003 classifier for identification of breast cancer...

ssp2006: SSP2006 classifier for identification of breast cancer...

stab.fs: Function to quantify stability of feature selection.

stab.fs.ranking: Function to quantify stability of feature ranking.

st.gallen: Function to compute the St Gallen consensus criterion for...

strescR: Utility function to escape LaTeX special characters present...

subtype.cluster: Function to fit the Subtype Clustering Model

subtype.cluster.predict: Function to identify breast cancer molecular subtypes using...

tamr13: Function to compute the risk scores of the tamoxifen...

tbrm: Function to compute Tukey's Biweight Robust Mean

vdxs: Gene expression, annotations and clinical data from Wang et...

weighted.meanvar: Function to compute the weighted mean and weighted variance...

write.m.file: Function to write a 'csv' file containing gene lists (aka...

Files in this package

genefu/DESCRIPTION
genefu/NAMESPACE
genefu/R
genefu/R/SpearmanCI.R genefu/R/bimod.R genefu/R/boxplotplus2.R genefu/R/claudinLow.R genefu/R/collapseIDs.R genefu/R/compare.proto.cor.R genefu/R/compute.pairw.cor.meta.R genefu/R/compute.pairw.cor.z.R genefu/R/compute.proto.cor.meta.R genefu/R/cordiff.dep.R genefu/R/endoPredict.R genefu/R/fuzzy.ttest.R genefu/R/gene70.R genefu/R/gene76.R genefu/R/geneid.map.R genefu/R/genius.R genefu/R/ggi.R genefu/R/ihc4.R genefu/R/intrinsic.cluster.R genefu/R/intrinsic.cluster.predict.R genefu/R/map.datasets.R genefu/R/medianCtr.R genefu/R/molecular.subtyping.R genefu/R/npi.R genefu/R/oncotypedx.R genefu/R/ovcAngiogenic.R genefu/R/ovcCrijns.R genefu/R/ovcSigs.R genefu/R/ovcTCGA.R genefu/R/ovcYoshihara.R genefu/R/overlapSets.R genefu/R/pik3cags.R genefu/R/power.cor.R genefu/R/ps.cluster.R genefu/R/read.m.file.R genefu/R/readArray.R genefu/R/rename.duplicate.R genefu/R/rescale.R genefu/R/rorS.R genefu/R/setcolclass.df.R genefu/R/sig.score.R genefu/R/st.gallen.R genefu/R/stab.fs.R genefu/R/stab.fs.ranking.R genefu/R/strescR.R genefu/R/subtype.cluster.R genefu/R/subtype.cluster.predict.R genefu/R/tamr13.R genefu/R/tbrm.R genefu/R/weighted.meanvar.R genefu/R/write.m.file.R
genefu/README
genefu/build
genefu/build/genefu.pdf
genefu/build/vignette.rds
genefu/data
genefu/data/claudinLowData.rda
genefu/data/datalist
genefu/data/expos.rda
genefu/data/mod1.rda
genefu/data/mod2.rda
genefu/data/modelOvcAngiogenic.rda
genefu/data/nkis.rda
genefu/data/pam50.rda
genefu/data/pam50.robust.rda
genefu/data/pam50.scale.rda
genefu/data/scmgene.robust.rda
genefu/data/scmod1.robust.rda
genefu/data/scmod2.robust.rda
genefu/data/sig.endoPredict.rda
genefu/data/sig.gene70.rda
genefu/data/sig.gene76.rda
genefu/data/sig.genius.rda
genefu/data/sig.ggi.rda
genefu/data/sig.oncotypedx.rda
genefu/data/sig.pik3cags.rda
genefu/data/sig.tamr13.rda
genefu/data/sigOvcAngiogenic.rda
genefu/data/sigOvcCrijns.rda
genefu/data/sigOvcSpentzos.rda
genefu/data/sigOvcTCGA.rda
genefu/data/sigOvcYoshihara.rda
genefu/data/ssp2003.rda
genefu/data/ssp2003.robust.rda
genefu/data/ssp2003.scale.rda
genefu/data/ssp2006.rda
genefu/data/ssp2006.robust.rda
genefu/data/ssp2006.scale.rda
genefu/data/vdxs.rda
genefu/inst
genefu/inst/doc
genefu/inst/doc/genefu.R
genefu/inst/doc/genefu.Rnw
genefu/inst/doc/genefu.pdf
genefu/inst/extdata
genefu/inst/extdata/T.E.9CELL-LINE.txt
genefu/inst/extdata/bentink2012_angiogenic.csv
genefu/inst/extdata/crijns2009_sig.csv
genefu/inst/extdata/desmedt2008_genemodules.csv
genefu/inst/extdata/filipits2011_sig_endopredict.csv
genefu/inst/extdata/haibekains2009_sig_genius.csv
genefu/inst/extdata/loi2008_tamr13.csv
genefu/inst/extdata/loi2010_pik3cags.csv
genefu/inst/extdata/paik2004_sig_oncotypedx.csv
genefu/inst/extdata/pam50_model.csv
genefu/inst/extdata/scmgene_robust_model.csv
genefu/inst/extdata/scmod1_robust_model.csv
genefu/inst/extdata/scmod2_robust_model.csv
genefu/inst/extdata/sotiriou2006_sig_ggi.csv
genefu/inst/extdata/spentzos2011_sig.csv
genefu/inst/extdata/ssp2003_model.csv
genefu/inst/extdata/ssp2006_model.csv
genefu/inst/extdata/tcga2011_sig.csv
genefu/inst/extdata/veer2002_sig_gene70.csv
genefu/inst/extdata/wang2005_sig_gene76.csv
genefu/inst/extdata/wirapati2008_genemodules.csv
genefu/inst/extdata/yoshihara2010_sig.csv
genefu/man
genefu/man/bimod.Rd genefu/man/boxplotplus2.Rd genefu/man/claudinLow.Rd genefu/man/claudinLowData.Rd genefu/man/collapseIDs.Rd genefu/man/compare.proto.cor.Rd genefu/man/compute.pairw.cor.meta.Rd genefu/man/compute.pairw.cor.z.Rd genefu/man/compute.proto.cor.meta.Rd genefu/man/cordiff.dep.Rd genefu/man/endoPredict.Rd genefu/man/expos.Rd genefu/man/fuzzy.ttest.Rd genefu/man/gene70.Rd genefu/man/gene76.Rd genefu/man/genefu-package.Rd genefu/man/geneid.map.Rd genefu/man/genius.Rd genefu/man/ggi.Rd genefu/man/ihc4.Rd genefu/man/intrinsic.cluster.Rd genefu/man/intrinsic.cluster.predict.Rd genefu/man/map.datasets.Rd genefu/man/medianCtr.Rd genefu/man/mod1.Rd genefu/man/mod2.Rd genefu/man/modelOvcAngiogenic.Rd genefu/man/molecular.subtyping.Rd genefu/man/nkis.Rd genefu/man/npi.Rd genefu/man/oncotypedx.Rd genefu/man/ovcAngiogenic.Rd genefu/man/ovcCrijns.Rd genefu/man/ovcTCGA.Rd genefu/man/ovcYoshihara.Rd genefu/man/overlapSets.Rd genefu/man/pam50.Rd genefu/man/pik3cags.Rd genefu/man/power.cor.Rd genefu/man/ps.cluster.Rd genefu/man/read.m.file.Rd genefu/man/readArray.Rd genefu/man/rename.duplicate.Rd genefu/man/rescale.Rd genefu/man/rorS.Rd genefu/man/scmgene.robust.Rd genefu/man/scmod1.robust.Rd genefu/man/scmod2.robust.Rd genefu/man/setcolclass.df.Rd genefu/man/sig.endoPredict.Rd genefu/man/sig.gene70.Rd genefu/man/sig.gene76.Rd genefu/man/sig.genius.Rd genefu/man/sig.ggi.Rd genefu/man/sig.oncotypedx.Rd genefu/man/sig.pik3cags.Rd genefu/man/sig.score.Rd genefu/man/sig.tamr13.Rd genefu/man/sigOvcAngiogenic.Rd genefu/man/sigOvcCrijns.Rd genefu/man/sigOvcSpentzos.Rd genefu/man/sigOvcTCGA.Rd genefu/man/sigOvcYoshihara.Rd genefu/man/spearmanCI.Rd genefu/man/ssp2003.Rd genefu/man/ssp2006.Rd genefu/man/st.gallen.Rd genefu/man/stab.fs.Rd genefu/man/stab.fs.ranking.Rd genefu/man/strescR.Rd genefu/man/subtype.cluster.Rd genefu/man/subtype.cluster.predict.Rd genefu/man/tamr13.Rd genefu/man/tbrm.Rd genefu/man/vdxs.Rd genefu/man/weighted.meanvar.Rd genefu/man/write.m.file.Rd
genefu/vignettes
genefu/vignettes/genefu.Rnw

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