| 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... |
