Computation of Gene Expression-Based Signatures in Breast Cancer

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... |

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