Tools for Connectivity Map-like analyses

annotate_eset_list | Function to complile a data frame with per-instance... |

camera_score-methods | Methods for Function 'camera_score' in Package 'gCMAP' |

center_eSet | A function to to center columns of eSet channels on either... |

CMAPCollection-class | Class '"CMAPCollection"' |

CMAPResults-class | Class '"CMAPResults"' |

connectivity_score-methods | Broad CMAP gene set enrichment metrics |

DESeq_nbinom | Function to perform a DESeq analysis to detect differential... |

eset_instances | A function to subset an eSet with expression data into... |

eSetOnDisk | A function to store the assayData of an eSet object as... |

featureScores-methods | Methods to obtain scores for CMAPCollection gene sets from a... |

fisher_score-methods | Hypergeometric probability of gene set enrichment |

gCMAPData-dataset | Example 'NChannelSet' |

gCMAP-package | Tools for Connectivity Map-like analyses |

geneIndex-methods | Methods for Function 'geneIndex' in Package 'gCMAP' |

generate_gCMAP_NChannelSet | Generate a perturbation profile library from expression sets... |

GeneSet-methods | Methods for 'GeneSet' and 'GeneColorSet' |

gsealm_jg_score-methods | Parametric test for testing normally distributed scores for... |

gsealm_score-methods | Methods for Function 'gsealm_score' in Package 'gCMAP' |

induceCMAPCollection-methods | Methods for Function 'induceCMAPCollection' in Package... |

KEGG2cmap | Functions to generate species-specific CMAPCollections from... |

mapNmerge | A function to map eSet featureNames and calculate summaries... |

matrix_or_big.matrix-class | Class '"matrix_or_big.matrix"' |

memorize | Create a new NChannelSet instance by selecting specific... |

mergeCMAPs | This function merged two eSets. |

mgsa_score-methods | Model-based gene set analysis (MGSA) |

minSetSize-methods | GeneSetCollection length filtering |

mroast_score-methods | Methods for Function 'mroast_score' in Package 'gCMAP' |

pairwise_compare | Generate statistics associated with pairwise differential... |

pairwise_DESeq | Generate statistics associated with pairwise differential... |

romer_score-methods | Methods for Function 'romer_score' in Package 'gCMAP' |

SignedGeneSet-class | Class '"SignedGeneSet"' |

SignedGeneSet-methods | Construtor for SignedGeneSet |

signedRankSumTest | An implementation of the Wilcox rank sum test / Mann-Whitney... |

splitPerturbations | Function to split an ExpressionSet downloaded from... |

wilcox_score-methods | Methods for Function 'wilcox_score' in Package 'gCMAP' |

zScores | Function to calculate z-scores from p-values |

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