gCMAP
Tools for Connectivity Map-like analyses

Package index
Search the gCMAP package
Vignettes
Functions
298
Source code
25
Man pages
36
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gCMAP: Tools for Connectivity Map-like analyses
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API

API for gCMAP
Tools for Connectivity Map-like analyses

Global functions
.DESeq_nbinom Man page Source code
.S Source code
.annotatedDataFrameFromMatrix Source code
.assayDataDimnames Source code
.f_checkpackage Source code
.foldChange Source code
.harmonizeDimnames Source code
.jg Source code
.ks Source code
.lookupAnno Source code
.moderated_logFC Source code
.onAttach Source code
.overview.density Source code
.overview.heatmap Source code
.probeAnno Source code
.process_arrays Source code
.process_counts Source code
.s Source code
.vst_transform Source code
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
GeneColorSet,NChannelSet-method Man page
GeneSet Man page
GeneSet,NChannelSet-method Man page
KEGG2cmap Man page Source code
S Man page
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
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
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
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
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
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
ks Man page
labels Man page
labels,CMAPResults-method Man page
labels<- Man page
labels<-,CMAPResults-method Man page
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
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
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
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
plot,CMAPResults,ANY-method Man page
pval Man page
pval,CMAPResults-method Man page
pval<- Man page
pval<-,CMAPResults-method Man page
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
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<- 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
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
gCMAP documentation built on April 29, 2020, 3:54 a.m.

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