Function to estimate whether two dependent correlations differ
PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.
Function to identify bimodality for gene expression or signature score
Function to rename duplicated strings.
Function to statistically compare correlation to prototypes
Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.
Overlap two datasets
Function to compute the St Gallen consensus criterion for prognostication
Function to set the class of columns in a data.frame
Gene expression, annotations and clinical data from van de Vijver et al. 2002
Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer.
Function to compute the Relapse Score as published by Wang et al. 2005
Function to compute the PIK3CA gene signature (PIK3CA-GS)
Function to compute the subtype scores and risk classifications for the prognostic signature published by Yoshihara et al.
Function to compute correlations to prototypes in a meta-analytical framework
Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002
Model used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.
Signature used to compute the OncotypeDX signature as published by Paik et al 2004
Function to rescale values based on quantiles
Signature used to compute the endoPredict signature as published by Filipits et al 2011
Function to compute the rorS signature as published by Parker et al 2009
Function to quantify stability of feature selection.
Function to compute the subtype scores and risk classifications for the prognostic signature published by Crinjs et al.
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Function to compute the risk scores of the tamoxifen resistance signature (TAMR13)
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Function to compute the weighted mean and weighted variance of 'x'
Subtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes
SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
Box plot of group of values with corresponding jittered points
Function to quantify stability of feature ranking.
Function to write a 'csv' file containing gene lists (aka gene signatures)
Function to compute the Z transformation of the pairwise correlations for a list of datasets
Function to compute the endoPredict signature as published by Filipits et al 2011
Function to compute pairwise correlations in a meta-analytical framework
Function to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002
Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Wirapati et al 2008)
Function to compute the confidence interval for the Spearman correelation coefficient
Function to compute signature scores as linear combination of gene expressions
Function to fit the Subtype Clustering Model
Center around the median
Gene modules published in Wirapati et al. 2008
Function to find the common genes between two datasets or a dataset and a gene list
Function to compute the subtype scores and risk classifications for the angiogenic molecular subtype in ovarian cancer
Subtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)
Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006
Function to compute the raw and scaled Gene expression Grade Index (GGI)
Function to compute the OncotypeDX signature as published by Paik et al. in 2004.
Function to compute the prediction scores and risk classifications for the ovarian cancer TCGA signature
Overlap two datasets
Function to identify breast cancer molecular subtypes using the Subtype Clustering Model
Gene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
Function to compute Tukey's Biweight Robust Mean
claudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.
Function to compute the Nottingham Prognostic Index
Function to read a 'csv' file containing gene lists (aka gene signatures)
Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005
Function to compute the prediction strength of a clustering model
intrinsic.cluster.predict
Function to identify breast cancer molecular subtypes using the Single Sample Predictor (SSP)
Function to compute the fuzzy Student t test based on weighted mean and weighted variance
Gene modules published in Desmedt et al. 2008
Function to map a list of datasets through EntrezGene IDs in order to get the union of the genes
Gene expression Grade Index (GGI) as published in Sotiriou et al. 2006
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Gene expression, annotations and clinical data from the International Genomics Consortium
SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
Utility function to collapse IDs
Function to compute the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010
Claudin-low classification for Breast Cancer Data
Function to identify breast cancer molecular subtypes using the Subtype Clustering Model
Function to compute the IHC4 prognostic score as published by Paik et al. in 2004.
Function to fit a Single Sample Predictor (SSP) as in Perou, Sorlie, Hu, and Parker publications
Function for sample size calculation for correlation coefficients
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Utility function to escape LaTeX special characters present in a string