API for Bioconductor-mirror/gCMAP
Tools for Connectivity Map-like analyses

Global functions
.DESeq_nbinom Man page
CMAPCollection Man page
CMAPCollection,Matrix-method Man page
CMAPCollection,environment-method Man page
CMAPCollection,matrix-method Man page
CMAPCollection,missing-method Man page
CMAPCollection-class Man page
CMAPResults Man page
CMAPResults-class Man page
DESeq_nbinom Source code
GeneColorSet,NChannelSet-method Man page
GeneSet Man page
GeneSet,NChannelSet-method Man page
KEGG2cmap Man page Source code
S Man page Source code
SignedGeneSet Man page
SignedGeneSet,ANY-method Man page
SignedGeneSet,missing-method Man page
SignedGeneSet-class Man page
addFeatureData Source code
annotate_eset_list Man page Source code
annotatedDataFrameFromMatrix Source code
assayDataDimnames Source code
assayDataSubsetElements Source code Source code
camera_score Man page
camera_score,eSet,CMAPCollection-method Man page
camera_score,eSet,GeneSet-method Man page
camera_score,eSet,GeneSetCollection-method Man page
camera_score,matrix,CMAPCollection-method Man page
camera_score,matrix,GeneSet-method Man page
camera_score,matrix,GeneSetCollection-method Man page
camera_score-methods Man page
center.function Source code
center_eSet Man page Source code
cmapTable Man page
cmapTable,CMAPResults-method Man page
connectivity_score Man page
connectivity_score,ANY,GeneSet-method Man page
connectivity_score,eSet,CMAPCollection-method Man page
connectivity_score,eSet,GeneSetCollection-method Man page
connectivity_score,eSet,SignedGeneSet-method Man page
connectivity_score,matrix,CMAPCollection-method Man page
connectivity_score,matrix,GeneSetCollection-method Man page
connectivity_score,matrix,SignedGeneSet-method Man page
docs Man page
docs,CMAPResults-method Man page
docs<- Man page
docs<-,CMAPResults-method Man page
downIds Man page
downIds,CMAPCollection-method Man page
downIds,SignedGeneSet-method Man page
eSetOnDisk Man page Source code
eSetProbeToGene Source code
effect Man page
effect,CMAPResults-method Man page
effect<- Man page
effect<-,CMAPResults-method Man page
errors Man page
errors,CMAPResults-method Man page
errors<- Man page
errors<-,CMAPResults-method Man page
eset_instances Man page Source code
f_checkpackage Source code
featureScores Man page
featureScores,BigMatrix,CMAPCollection-method Man page
featureScores,CMAPCollection,BigMatrix-method Man page
featureScores,CMAPCollection,CMAPCollection-method Man page
featureScores,CMAPCollection,eSet-method Man page
featureScores,CMAPCollection,matrix-method Man page
featureScores,CMAPCollection,matrix_or_big.matrix-method Man page
featureScores,CMAPCollection,numeric-method Man page
featureScores,eSet,CMAPCollection-method Man page
featureScores,matrix,CMAPCollection-method Man page
featureScores,matrix_or_big.matrix,CMAPCollection-method Man page
featureScores,numeric,CMAPCollection-method Man page
featureScores-methods Man page
fisher_p Source code
fisher_score Man page
fisher_score,CMAPCollection,CMAPCollection,character-method Man page
fisher_score,CMAPCollection,GeneSetCollection,character-method Man page
fisher_score,CMAPCollection,NChannelSet,character-method Man page
fisher_score,GeneSet,CMAPCollection,character-method Man page
fisher_score,GeneSet,GeneSet,character-method Man page
fisher_score,GeneSet,GeneSetCollection,character-method Man page
fisher_score,GeneSet,NChannelSet,character-method Man page
fisher_score,GeneSetCollection,CMAPCollection,character-method Man page
fisher_score,GeneSetCollection,GeneSetCollection,character-metho Man page
fisher_score,GeneSetCollection,NChannelSet,character-method Man page
fisher_score,SignedGeneSet,CMAPCollection,character-method Man page
fisher_score,SignedGeneSet,NChannelSet,character-method Man page
fisher_score-methods Man page
foldChange Source code Source code
gCMAP Man page
gCMAP-package Man page
gCMAPData Man page
geneIds,CMAPCollection-method Man page
geneIndex Man page
geneIndex,CMAPCollection,character-method Man page
geneIndex,GeneSet,character-method Man page
geneIndex,GeneSetCollection,character-method Man page
geneIndex-methods Man page
geneScores Man page
geneScores,CMAPResults-method Man page
geneSign Man page
geneSign,SignedGeneSet-method Man page
geneSign<- Man page
geneSign<-,SignedGeneSet,character-method Man page
geneSign<-,SignedGeneSet,factor-method Man page
generate_gCMAP_NChannelSet Man page Source code
go2cmap Man page Source code
gsNormalize Source code
gsealmPerm Source code
gsealm_jg_score Man page
gsealm_jg_score,CMAPCollection,eSet-method Man page
gsealm_jg_score,CMAPCollection,matrix-method Man page
gsealm_jg_score,CMAPCollection,numeric-method Man page
gsealm_jg_score,GeneSet,eSet-method Man page
gsealm_jg_score,GeneSet,matrix-method Man page
gsealm_jg_score,GeneSet,numeric-method Man page
gsealm_jg_score,GeneSetCollection,eSet-method Man page
gsealm_jg_score,GeneSetCollection,matrix-method Man page
gsealm_jg_score,GeneSetCollection,numeric-method Man page
gsealm_jg_score,eSet,CMAPCollection-method Man page
gsealm_jg_score,eSet,GeneSet-method Man page
gsealm_jg_score,eSet,GeneSetCollection-method Man page
gsealm_jg_score,matrix,GeneSet-method Man page
gsealm_jg_score,matrix,GeneSetCollection-method Man page
gsealm_jg_score,matrix_or_big.matrix,CMAPCollection-method Man page
gsealm_jg_score,numeric,CMAPCollection-method Man page
gsealm_jg_score,numeric,GeneSet-method Man page
gsealm_jg_score,numeric,GeneSetCollection-method Man page
gsealm_jg_score-methods Man page
gsealm_score Man page
gsealm_score,ExpressionSet,CMAPCollection-method Man page
gsealm_score,ExpressionSet,GeneSet-method Man page
gsealm_score,ExpressionSet,GeneSetCollection-method Man page
gsealm_score,eSet,CMAPCollection-method Man page
gsealm_score,eSet,GeneSet-method Man page
gsealm_score,eSet,GeneSetCollection-method Man page
gsealm_score,matrix,CMAPCollection-method Man page
gsealm_score,matrix,GeneSet-method Man page
gsealm_score,matrix,GeneSetCollection-method Man page
gsealm_score-methods Man page
harmonizeDimnames Source code
incidence,CMAPCollection-method Man page
incidence,GeneSetCollection-method Man page
incidence,SignedGeneSet-method Man page
incidence,list-method Man page
induceCMAPCollection Man page
induceCMAPCollection,eSet-method Man page
induceCMAPCollection,matrix-method Man page
induceCMAPCollection-methods Man page
initialize,CMAPCollection-method Man page
initialize,CMAPResults-method Man page
initialize,SignedGeneSet-method Man page
jg Source code
ks Man page Source code
labels Man page
labels,CMAPResults-method Man page
labels<- Man page
labels<-,CMAPResults-method Man page
lookupAnno Source code
mapIdentifiers,SignedGeneSet,GeneIdentifierType,GeneIdentifierTy Man page
mapIdentifiers,SignedGeneSet,GeneIdentifierType,missing-method Man page
mapIdentifiers,SignedGeneSet,missing,ANY-method Man page
mapNmerge Man page Source code
matrix_or_big.matrix-class Man page
members Man page
members,CMAPCollection-method Man page
memorize Man page Source code
mergeCMAPs Man page Source code
mergeCollections Man page
mergeCollections,CMAPCollection,CMAPCollection-method Man page
mgsa_score Man page
mgsa_score,CMAPCollection,CMAPCollection,character-method Man page
mgsa_score,CMAPCollection,GeneSetCollection,character-method Man page
mgsa_score,GeneSet,CMAPCollection,character-method Man page
mgsa_score,GeneSet,GeneSet,character-method Man page
mgsa_score,GeneSet,GeneSetCollection,character-method Man page
mgsa_score,GeneSet,NChannelSet,character-method Man page
mgsa_score,GeneSetCollection,CMAPCollection,character-method Man page
mgsa_score,GeneSetCollection,GeneSetCollection,character-method Man page
mgsa_score,GeneSetCollection,NChannelSet,character-method Man page
mgsa_score,SignedGeneSet,CMAPCollection,character-method Man page
mgsa_score,SignedGeneSet,NChannelSet,character-method Man page
mgsa_score-methods Man page
minSetSize Man page
minSetSize,CMAPCollection-method Man page
moderated_logFC Source code
mroast_score Man page
mroast_score,eSet,CMAPCollection-method Man page
mroast_score,eSet,GeneSet-method Man page
mroast_score,eSet,GeneSetCollection-method Man page
mroast_score,matrix,CMAPCollection-method Man page
mroast_score,matrix,GeneSet-method Man page
mroast_score,matrix,GeneSetCollection-method Man page
mroast_score-methods Man page
nFound Man page
nFound,CMAPResults-method Man page
nFound<- Man page
nFound<-,CMAPResults-method Man page
nSet Man page
nSet,CMAPResults-method Man page
nSet<- Man page
nSet<-,CMAPResults-method Man page
ncidence Source code
overview.density Source code
overview.heatmap Source code
padj Man page
padj,CMAPResults-method Man page
padj<- Man page
padj<-,CMAPResults-method Man page
pairwise_DESeq Man page Source code
pairwise_compare Man page Source code
pairwise_compare_limma Man page Source code
pickChannels Source code
plot,CMAPResults,ANY-method Man page
probeAnno Source code
process_arrays Source code
process_counts Source code
pval Man page
pval,CMAPResults-method Man page
pval<- Man page
pval<-,CMAPResults-method Man page
pvalFromPermMat Source code
reactome2cmap Man page Source code
romer_score Man page
romer_score,eSet,CMAPCollection-method Man page
romer_score,eSet,GeneSet-method Man page
romer_score,eSet,GeneSetCollection-method Man page
romer_score,matrix,CMAPCollection-method Man page
romer_score,matrix,GeneSet-method Man page
romer_score,matrix,GeneSetCollection-method Man page
romer_score-methods Man page
s Man page Source code
set Man page
set,CMAPResults-method Man page
set<- Man page
set<-,CMAPResults-method Man page
setSizes Man page
setSizes,CMAPCollection-method Man page
show,CMAPResults-method Man page
show,SignedGeneSet-method Man page
signed Man page
signed,CMAPCollection-method Man page
signed.incidence Source code
signed<- Man page
signed<-,CMAPCollection-method Man page
signedRankSumTest Man page Source code
splitPerturbations Man page Source code
trend Man page
trend,CMAPResults-method Man page
trend<- Man page
trend<-,CMAPResults-method Man page
upIds Man page
upIds,CMAPCollection-method Man page
upIds,SignedGeneSet-method Man page
vst_transform Source code
wiki2cmap Man page Source code
wilcox_score Man page
wilcox_score,CMAPCollection,eSet-method Man page
wilcox_score,CMAPCollection,matrix-method Man page
wilcox_score,CMAPCollection,numeric-method Man page
wilcox_score,GeneSet,eSet-method Man page
wilcox_score,GeneSet,matrix-method Man page
wilcox_score,GeneSet,numeric-method Man page
wilcox_score,GeneSetCollection,eSet-method Man page
wilcox_score,GeneSetCollection,matrix-method Man page
wilcox_score,GeneSetCollection,numeric-method Man page
wilcox_score,eSet,CMAPCollection-method Man page
wilcox_score,eSet,GeneSet-method Man page
wilcox_score,eSet,GeneSetCollection-method Man page
wilcox_score,matrix,CMAPCollection-method Man page
wilcox_score,matrix,GeneSet-method Man page
wilcox_score,matrix,GeneSetCollection-method Man page
wilcox_score,numeric,CMAPCollection-method Man page
wilcox_score,numeric,GeneSet-method Man page
wilcox_score,numeric,GeneSetCollection-method Man page
wilcox_score-methods Man page Man page
zScores Man page Source code
zscores Man page
zscores,CMAPResults-method Man page
Bioconductor-mirror/gCMAP documentation built on June 1, 2017, 8:46 a.m.