Man pages for gCMAP
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 |
