bimod                   Function to identify bimodality for gene
                        expression or signature score
boxplotplus2            Box plot of group of values with corresponding
                        jittered points
compare.proto.cor       Function to statistically compare correlation
                        to prototypes
compute.pairw.cor.meta
                        Function to compute pairwise correlations in a
                        meta-analytical framework
compute.pairw.cor.z     Function to compute the Z transformation of the
                        pairwise correlations for a list of datasets
compute.proto.cor.meta
                        Function to compute correlations to prototypes
                        in a meta-analytical framework
cordiff.dep             Function to estimate whether two dependent
                        correlations differ
gene70                  Function to compute the 70 genes prognosis
                        profile (GENE70) as published by van't Veer et
                        al. 2002
gene76                  Function to compute the Relapse Score as
                        published by Wang et al. 2005
genefu-package          Relevant Functions for Gene Expression
                        Analysis, Especially in Breast Cancer.
geneid.map              Function to find the common genes between two
                        datasets or a dataset and a gene list
genius                  Function to compute the Gene Expression
                        progNostic Index Using Subtypes (GENIUS) as
                        published by Haibe-Kains et al. 2009
ggi                     Function to compute the raw and scaled Gene
                        expression Grade Index (GGI)
intrinsic.cluster       Function to fit a Single Sample Predictor (SSP)
                        as in Perou, Sorlie, Hu, and Parker
                        publications
intrinsic.cluster.predict
                        Function to identify breast cancer molecular
                        subtypes using the Single Sample Predictor
                        (SSP)
map.datasets            Function to map a list of datasets through
                        EntrezGene IDs in order to get the union of the
                        genes
mod1                    Gene modules published in Desmedt et al. 2008
mod2                    Gene modules published in Wirapati et al. 2008
nki                     Gene expression, annotations and clinical data
                        from van de Vijver et al. 2002
npi                     Function to compute the Nottingham Prognostic
                        Index
pam50                   PAM50 classifier for identification of breast
                        cancer molecular subtypes (Parker et al 2009)
ps.cluster              Function to compute the prediction strength of
                        a clustering model
read.m.file             Function to read a 'csv' file containing gene
                        lists (aka gene signatures)
rescale                 Function to rescale values based on quantiles
sbtgene                 Subtype Clustering Model using only ESR1, ERBB2
                        and AURKA genes for identification of breast
                        cancer molecular subtypes
sbtmod1                 Subtype Clustering Model using ESR1, ERBB2 and
                        AURKA modules for identification of breast
                        cancer molecular subtypes (Desmedt et al 2008)
sbtmod2                 Subtype Clustering Model using ESR1, ERBB2 and
                        AURKA modules for identification of breast
                        cancer molecular subtypes (Wirapati et al 2008)
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.
                        2009
sig.ggi                 Gene expression Grade Index (GGI) as published
                        in Sotiriou et al. 2006
sig.score               Function to compute signature scores as linear
                        combination of gene expressions
ssp2003                 SSP2003 classifier for identification of breast
                        cancer molecular subtypes (Sorlie et al 2003)
ssp2006                 SSP2006 classifier for identification of breast
                        cancer molecular subtypes (Hu et al 2006)
st.gallen               Function to compute the St Gallen consensus
                        criterion for prognostication
subtype.cluster         Function to fit the Subtype Clustering Model
subtype.cluster.predict
                        Function to identify breast cancer molecular
                        subtypes using the Subtype Clustering Model
tbrm                    Function to compute Tukey's Biweight Robust
                        Mean
vdx                     Gene expression, annotations and clinical data
                        from Wang et al. 2005 and Minn et al 2007
write.m.file            Function to write a 'csv' file containing gene
                        lists (aka gene signatures)
