Clustering Enrichment Analysis

annotateChipSeqPeaks | Function to match each peaks to associated genes in terms of... |

bCa | Sets of p-values derived from two breast cancer data sets. |

call.treeview | Function to call the standalone fTreeView Java application |

cdt2r | Functions to import files in TreeView format into R. |

chipSeqWeightedSum | Calculate binding strengh by summing weighted chip-seq peaks. |

CLEAN-package | Clustering Enrichment Analysis |

cMap | A set of p-values derived from the Connectivity Map dataset. |

convertFunctionalCategories | Function to convert Entrez gene ID-based functional... |

createRefGenome | Function to match download ref genome platform from UCSC. |

generateTreeViewFiles | Wrapper function to perform functional Clustering Enrichment... |

geneSigInClustering | Auxiliary functions to funcClustAnnot and geneListEnrichment |

genesInEnrichedCategories | Function to intersect a gene list with enriched categories |

getBinarySubTree | Get the left or right subtree of a given hierarchical... |

getFuntionalCategories | Retrieve functional categories from species-specific library. |

gimmOut | An gimmR object, i.e. a list containing a dataframe with gene... |

GRS | Function to calculate the Generalized Random Set statistic to... |

LRpath | Testing GO terms or KEGG with logistic regression |

nonHierarchicalClustering | Convert a non-hierarchical clustering into hierarchical... |

plotCLEANscore | Function to generate a diagnostic plot using the CLEAN score |

qvalue | Estimate the q-values for a given set of p-values |

r2cdt | Functions to generate fTreeView files |

RandomSet | Testing GO terms, KEGG pathways, and other categories with... |

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