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A C D E F G I K L M N P R S T U W Z misc
| gCMAP-package | Tools for Connectivity Map-like analyses |
| annotate_eset_list | Function to complile a data frame with per-instance annotation for a list of eSet objects generated by the 'splitPerturbations' function. The output can be used directly as sample.annotation for the 'NChannelSet' function. |
| camera_score | Methods for Function 'camera_score' in Package 'gCMAP' |
| camera_score-method | Methods for Function 'camera_score' in Package 'gCMAP' |
| camera_score-methods | Methods for Function 'camera_score' in Package 'gCMAP' |
| center_eSet | A function to to center columns of eSet channels on either their kernel density peak, their mean or their median. |
| CMAPCollection | Class '"CMAPCollection"' |
| CMAPCollection-class | Class '"CMAPCollection"' |
| CMAPCollection-method | Class '"CMAPCollection"' |
| CMAPResults | Class '"CMAPResults"' |
| CMAPResults-class | Class '"CMAPResults"' |
| cmapTable | Class '"CMAPResults"' |
| cmapTable-method | Class '"CMAPResults"' |
| connectivity_score | Broad CMAP gene set enrichment metrics |
| connectivity_score-method | Broad CMAP gene set enrichment metrics |
| docs | Class '"CMAPResults"' |
| docs-method | Class '"CMAPResults"' |
| docs<- | Class '"CMAPResults"' |
| docs<--method | Class '"CMAPResults"' |
| downIds | Class '"SignedGeneSet"' |
| downIds-method | Class '"CMAPCollection"' |
| downIds-method | Class '"SignedGeneSet"' |
| effect | Class '"CMAPResults"' |
| effect-method | Class '"CMAPResults"' |
| effect<- | Class '"CMAPResults"' |
| effect<--method | Class '"CMAPResults"' |
| errors | Class '"CMAPResults"' |
| errors-method | Class '"CMAPResults"' |
| errors<- | Class '"CMAPResults"' |
| errors<--method | Class '"CMAPResults"' |
| eSetOnDisk | A function to store the assayData of an eSet object as BigMatrix files on disk. |
| eset_instances | A function to subset an eSet with expression data into smaller datasets, each corresponding to a single perturbation experiment. |
| featureScores | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet |
| featureScores-method | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet |
| featureScores-methods | Methods to obtain scores for CMAPCollection gene sets from a matrix or eSet |
| fisher_score | Hypergeometric probability of gene set enrichment |
| fisher_score-method | Hypergeometric probability of gene set enrichment |
| fisher_score-methods | Hypergeometric probability of gene set enrichment |
| gCMAP | Tools for Connectivity Map-like analyses |
| gCMAPData | Example 'NChannelSet' |
| GeneColorSet-method | Methods for 'GeneSet' and 'GeneColorSet' |
| geneIds-method | Class '"CMAPCollection"' |
| geneIndex | Methods for Function 'geneIndex' in Package 'gCMAP' |
| geneIndex-method | Methods for Function 'geneIndex' in Package 'gCMAP' |
| geneIndex-methods | Methods for Function 'geneIndex' in Package 'gCMAP' |
| generate_gCMAP_NChannelSet | Generate a perturbation profile library from expression sets of control/treatment pairs |
| geneScores | Class '"CMAPResults"' |
| geneScores-method | Class '"CMAPResults"' |
| GeneSet | Methods for 'GeneSet' and 'GeneColorSet' |
| GeneSet-method | Methods for 'GeneSet' and 'GeneColorSet' |
| geneSign | Class '"SignedGeneSet"' |
| geneSign-method | Class '"SignedGeneSet"' |
| geneSign<- | Class '"SignedGeneSet"' |
| geneSign<--method | Class '"SignedGeneSet"' |
| go2cmap | Functions to generate species-specific CMAPCollections from Bioconductor KEGG.db, reactome.db or GO.db annotation packages or the wikipathways <URL: http://www.wikipathways.org/index.php/Download_Pathways> project. |
| gsealm_jg_score | Parametric test for testing normally distributed scores for gene set enrichment |
| gsealm_jg_score-method | Parametric test for testing normally distributed scores for gene set enrichment |
| gsealm_jg_score-methods | Parametric test for testing normally distributed scores for gene set enrichment |
| gsealm_score | Methods for Function 'gsealm_score' in Package 'gCMAP' |
| gsealm_score-method | Methods for Function 'gsealm_score' in Package 'gCMAP' |
| gsealm_score-methods | Methods for Function 'gsealm_score' in Package 'gCMAP' |
| incidence-method | Class '"CMAPCollection"' |
| incidence-method | Class '"SignedGeneSet"' |
| induceCMAPCollection | Methods for Function 'induceCMAPCollection' in Package 'gCMAP' |
| induceCMAPCollection-method | Methods for Function 'induceCMAPCollection' in Package 'gCMAP' |
| induceCMAPCollection-methods | Methods for Function 'induceCMAPCollection' in Package 'gCMAP' |
| initialize-method | Class '"CMAPCollection"' |
| initialize-method | Class '"CMAPResults"' |
| initialize-method | Class '"SignedGeneSet"' |
| KEGG2cmap | Functions to generate species-specific CMAPCollections from Bioconductor KEGG.db, reactome.db or GO.db annotation packages or the wikipathways <URL: http://www.wikipathways.org/index.php/Download_Pathways> project. |
| ks | Broad CMAP gene set enrichment metrics |
| labels | Class '"CMAPResults"' |
| labels-method | Class '"CMAPResults"' |
| labels<- | Class '"CMAPResults"' |
| labels<--method | Class '"CMAPResults"' |
| mapIdentifiers-method | Class '"SignedGeneSet"' |
| mapNmerge | A function to map eSet featureNames and calculate summaries for many-to-one mapping features |
| matrix_or_big.matrix-class | Class '"matrix_or_big.matrix"' |
| members | Class '"CMAPCollection"' |
| members-method | Class '"CMAPCollection"' |
| memorize | Create a new NChannelSet instance by selecting specific channels and load BigMatrix assayData into memory. |
| mergeCMAPs | This function merged two eSets. |
| mergeCollections | Class '"CMAPCollection"' |
| mergeCollections-method | Class '"CMAPCollection"' |
| mgsa_score | Model-based gene set analysis (MGSA) |
| mgsa_score-method | Model-based gene set analysis (MGSA) |
| mgsa_score-methods | Model-based gene set analysis (MGSA) |
| minSetSize | GeneSetCollection length filtering |
| minSetSize-method | GeneSetCollection length filtering |
| mroast_score | Methods for Function 'mroast_score' in Package 'gCMAP' |
| mroast_score-method | Methods for Function 'mroast_score' in Package 'gCMAP' |
| mroast_score-methods | Methods for Function 'mroast_score' in Package 'gCMAP' |
| nFound | Class '"CMAPResults"' |
| nFound-method | Class '"CMAPResults"' |
| nFound<- | Class '"CMAPResults"' |
| nFound<--method | Class '"CMAPResults"' |
| nSet | Class '"CMAPResults"' |
| nSet-method | Class '"CMAPResults"' |
| nSet<- | Class '"CMAPResults"' |
| nSet<--method | Class '"CMAPResults"' |
| padj | Class '"CMAPResults"' |
| padj-method | Class '"CMAPResults"' |
| padj<- | Class '"CMAPResults"' |
| padj<--method | Class '"CMAPResults"' |
| pairwise_compare | Generate statistics associated with pairwise differential expression |
| pairwise_compare_limma | Generate statistics associated with pairwise differential expression |
| pairwise_DESeq | Generate statistics associated with pairwise differential expression from RNAseq count data |
| plot-method | Class '"CMAPResults"' |
| pval | Class '"CMAPResults"' |
| pval-method | Class '"CMAPResults"' |
| pval<- | Class '"CMAPResults"' |
| pval<--method | Class '"CMAPResults"' |
| reactome2cmap | Functions to generate species-specific CMAPCollections from Bioconductor KEGG.db, reactome.db or GO.db annotation packages or the wikipathways <URL: http://www.wikipathways.org/index.php/Download_Pathways> project. |
| romer_score | Methods for Function 'romer_score' in Package 'gCMAP' |
| romer_score-method | Methods for Function 'romer_score' in Package 'gCMAP' |
| romer_score-methods | Methods for Function 'romer_score' in Package 'gCMAP' |
| S | Broad CMAP gene set enrichment metrics |
| s | Broad CMAP gene set enrichment metrics |
| set | Class '"CMAPResults"' |
| set-method | Class '"CMAPResults"' |
| set<- | Class '"CMAPResults"' |
| set<--method | Class '"CMAPResults"' |
| setSizes | Class '"CMAPCollection"' |
| setSizes-method | Class '"CMAPCollection"' |
| show-method | Class '"CMAPResults"' |
| show-method | Class '"SignedGeneSet"' |
| signed | Class '"CMAPCollection"' |
| signed-method | Class '"CMAPCollection"' |
| signed<- | Class '"CMAPCollection"' |
| signed<--method | Class '"CMAPCollection"' |
| SignedGeneSet | Construtor for SignedGeneSet |
| SignedGeneSet-class | Class '"SignedGeneSet"' |
| SignedGeneSet-method | Construtor for SignedGeneSet |
| signedRankSumTest | An implementation of the Wilcox rank sum test / Mann-Whitney test that takes into account the direction / sign of gene set members and possibly the correlation between cases |
| splitPerturbations | Function to split an ExpressionSet downloaded from ArrayExpress based on the experimental factors present in the phenoData slot |
| trend | Class '"CMAPResults"' |
| trend-method | Class '"CMAPResults"' |
| trend<- | Class '"CMAPResults"' |
| trend<--method | Class '"CMAPResults"' |
| upIds | Class '"SignedGeneSet"' |
| upIds-method | Class '"CMAPCollection"' |
| upIds-method | Class '"SignedGeneSet"' |
| wiki2cmap | Functions to generate species-specific CMAPCollections from Bioconductor KEGG.db, reactome.db or GO.db annotation packages or the wikipathways <URL: http://www.wikipathways.org/index.php/Download_Pathways> project. |
| wilcox_score | Methods for Function 'wilcox_score' in Package 'gCMAP' |
| wilcox_score-method | Methods for Function 'wilcox_score' in Package 'gCMAP' |
| wilcox_score-methods | Methods for Function 'wilcox_score' in Package 'gCMAP' |
| zScores | Function to calculate z-scores from p-values |
| zscores | Class '"CMAPResults"' |
| zscores-method | Class '"CMAPResults"' |
| .DESeq_nbinom | Function to perform a DESeq analysis to detect differential expression between perturbation and control groups. |