Man pages for gCMAP
Tools for Connectivity Map-like analyses

annotate_eset_listFunction to complile a data frame with per-instance...
camera_score-methodsMethods for Function 'camera_score' in Package 'gCMAP'
center_eSetA function to to center columns of eSet channels on either...
CMAPCollection-classClass '"CMAPCollection"'
CMAPResults-classClass '"CMAPResults"'
connectivity_score-methodsBroad CMAP gene set enrichment metrics
DESeq_nbinomFunction to perform a DESeq analysis to detect differential...
eset_instancesA function to subset an eSet with expression data into...
eSetOnDiskA function to store the assayData of an eSet object as...
featureScores-methodsMethods to obtain scores for CMAPCollection gene sets from a...
fisher_score-methodsHypergeometric probability of gene set enrichment
gCMAPData-datasetExample 'NChannelSet'
gCMAP-packageTools for Connectivity Map-like analyses
geneIndex-methodsMethods for Function 'geneIndex' in Package 'gCMAP'
generate_gCMAP_NChannelSetGenerate a perturbation profile library from expression sets...
GeneSet-methodsMethods for 'GeneSet' and 'GeneColorSet'
gsealm_jg_score-methodsParametric test for testing normally distributed scores for...
gsealm_score-methodsMethods for Function 'gsealm_score' in Package 'gCMAP'
induceCMAPCollection-methodsMethods for Function 'induceCMAPCollection' in Package...
KEGG2cmapFunctions to generate species-specific CMAPCollections from...
mapNmergeA function to map eSet featureNames and calculate summaries...
matrix_or_big.matrix-classClass '"matrix_or_big.matrix"'
memorizeCreate a new NChannelSet instance by selecting specific...
mergeCMAPsThis function merged two eSets.
mgsa_score-methodsModel-based gene set analysis (MGSA)
minSetSize-methodsGeneSetCollection length filtering
mroast_score-methodsMethods for Function 'mroast_score' in Package 'gCMAP'
pairwise_compareGenerate statistics associated with pairwise differential...
pairwise_DESeqGenerate statistics associated with pairwise differential...
romer_score-methodsMethods for Function 'romer_score' in Package 'gCMAP'
SignedGeneSet-classClass '"SignedGeneSet"'
SignedGeneSet-methodsConstrutor for SignedGeneSet
signedRankSumTestAn implementation of the Wilcox rank sum test / Mann-Whitney...
splitPerturbationsFunction to split an ExpressionSet downloaded from...
wilcox_score-methodsMethods for Function 'wilcox_score' in Package 'gCMAP'
zScoresFunction to calculate z-scores from p-values
gCMAP documentation built on May 2, 2018, 4:17 a.m.