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in Desmedt et al. 2008", "topics": [ "mod1" ] }, { "page": "mod2", "title": "Gene modules published in Wirapati et al. 2008", "topics": [ "mod2" ] }, { "page": "modelOvcAngiogenic", "title": "Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.", "topics": [ "modelOvcAngiogenic" ] }, { "page": "molecular.subtyping", "title": "Function to identify breast cancer molecular subtypes using the Subtype Clustering Model", "topics": [ "molecular.subtyping" ] }, { "page": "nkis", "title": "Gene expression, annotations and clinical data from van de Vijver et al. 2002", "topics": [ "annot.nkis", "data.nkis", "demo.nkis", "nkis" ] }, { "page": "npi", "title": "Function to compute the Nottingham Prognostic Index", "topics": [ "npi" ] }, { "page": "oncotypedx", "title": "Function to compute the OncotypeDX signature as published by Paik et al. in 2004.", "topics": [ "oncotypedx" ] }, { "page": "ovcAngiogenic", "title": "Function to compute the subtype scores and risk classifications for the angiogenic molecular subtype in ovarian cancer", "topics": [ "ovcAngiogenic" ] }, { "page": "ovcCrijns", "title": "Function to compute the subtype scores and risk classifications for the prognostic signature published by Crinjs et al.", "topics": [ "ovcCrijns" ] }, { "page": "ovcTCGA", "title": "Function to compute the prediction scores and risk classifications for the ovarian cancer TCGA signature", "topics": [ "ovcTCGA" ] }, { "page": "ovcYoshihara", "title": "Function to compute the subtype scores and risk classifications for the prognostic signature published by Yoshihara et al.", "topics": [ "ovcYoshihara" ] }, { "page": "overlapSets", "title": "Overlap two datasets", "topics": [ "overlapSets" ] }, { "page": "pam50", "title": "PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)", "topics": [ "pam50", "pam50.robust", "pam50.scale" ] }, { "page": "pik3cags", "title": "Function to compute the PIK3CA gene signature (PIK3CA-GS)", "topics": [ "pik3cags" ] }, { "page": "power.cor", "title": "Function for sample size calculation for correlation coefficients", "topics": [ "power.cor" ] }, { "page": "ps.cluster", "title": "Function to compute the prediction strength of a clustering model", "topics": [ "ps.cluster" ] }, { "page": "read.m.file", "title": "Function to read a 'csv' file containing gene lists (aka gene signatures)", "topics": [ "read.m.file" ] }, { "page": "readArray", "title": "Overlap two datasets", "topics": [ "readArray" ] }, { "page": "rename.duplicate", "title": "Function to rename duplicated strings", "topics": [ "rename.duplicate" ] }, { "page": "rescale", "title": "Function to rescale values based on quantiles", "topics": [ "rescale" ] }, { "page": "rorS", "title": "Function to compute the rorS signature as published by Parker et al 2009", "topics": [ "rorS" ] }, { "page": "scmgene.robust", "title": "Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes", "topics": [ "scmgene.robust" ] }, { "page": "scmod1.robust", "title": "Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)", "topics": [ "scmod1.robust" ] }, { "page": "scmod2.robust", "title": "Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)", "topics": [ "scmod2.robust" ] }, { "page": "setcolclass.df", "title": "Function to set the class of columns in a data.frame", "topics": [ "setcolclass.df" ] }, { "page": "sig.endoPredict", "title": "Signature used to compute the endoPredict signature as published by Filipits et al 2011", "topics": [ "sig.endoPredict" ] }, { "page": "sig.gene70", "title": "Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002", "topics": [ "sig.gene70" ] }, { "page": "sig.gene76", "title": "Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005", "topics": [ "sig.gene76" ] }, { "page": "sig.genius", "title": "Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.", "topics": [ "sig.genius" ] }, { "page": "sig.ggi", "title": "Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006", "topics": [ "sig.ggi" ] }, { "page": "sig.oncotypedx", "title": "Signature used to compute the OncotypeDX signature as published by Paik et al 2004", "topics": [ "sig.oncotypedx" ] }, { "page": "sig.pik3cags", "title": "Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006", "topics": [ "sig.pik3cags" ] }, { "page": "sig.score", "title": "Function to compute signature scores as linear combination of gene expressions", "topics": [ "sig.score" ] }, { "page": "sig.tamr13", "title": "Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.", "topics": [ "sig.tamr13" ] }, { "page": "sigOvcAngiogenic", "title": "sigOvcAngiogenic dataset", "topics": [ "sigOvcAngiogenic" ] }, { "page": "sigOvcCrijns", "title": "sigOvcCrijns dataset", "topics": [ "sigOvcCrijns" ] }, { "page": "sigOvcSpentzos", "title": "sigOcvSpentzos dataset", "topics": [ "sigOvcSpentzos" ] }, { "page": "sigOvcTCGA", "title": "sigOvcTCGA dataset", "topics": [ "sigOvcTCGA" ] }, { "page": "sigOvcYoshihara", "title": "sigOvcYoshihara dataset", "topics": [ "sigOvcYoshihara" ] }, { "page": "spearmanCI", "title": "Function to compute the confidence interval for the Spearman correelation coefficient", "topics": [ "spearmanCI" ] }, { "page": "ssp2003", "title": "SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)", "topics": [ "ssp2003", "ssp2003.robust", "ssp2003.scale" ] }, { "page": "ssp2006", "title": "SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)", "topics": [ "ssp2006", "ssp2006.robust", "ssp2006.scale" ] }, { "page": "st.gallen", "title": "Function to compute the St Gallen consensus criterion for prognostication", "topics": [ "st.gallen" ] }, { "page": "stab.fs", "title": "Function to quantify stability of feature selection", "topics": [ "stab.fs" ] }, { "page": "stab.fs.ranking", "title": "Function to quantify stability of feature ranking", "topics": [ "stab.fs.ranking" ] }, { "page": "strescR", "title": "Utility function to escape LaTeX special characters present in a string", "topics": [ "strescR" ] }, { "page": "subtype.cluster", "title": "Function to fit the Subtype Clustering Model", "topics": [ "subtype.cluster" ] }, { "page": "subtype.cluster.predict", "title": "Function to identify breast cancer molecular subtypes using the Subtype Clustering Model", "topics": [ "subtype.cluster.predict" ] }, { "page": "tamr13", "title": "Function to compute the risk scores of the tamoxifen resistance signature (TAMR13)", "topics": [ "tamr13" ] }, { "page": "tbrm", "title": 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