Man pages for signatureSearch
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

append2H5Append Matrix to HDF5 File
cell_infoCell Type Information
chembl_moa_listMOA to Gene Mappings
clue_moa_listMOA to Drug Name Mappings
comp_fea_resPlot for Comparing Ranking Results of FEA Methods
create_empty_h5Create Empty HDF5 File
dim-methodsDimensions of an Object
drug_cell_ranksSummary ranking statistics across cell types
drugs10Drug Names Used in Examples
drugs-methodsExtract/Assign Drug Names for feaResult
dsea_GSEADrug Set Enrichment Analysis (DSEA) with GSEA Algorithm
dsea_hyperGDrug Set Enrichment Analysis (DSEA) with Hypergeometric Test
dtnetplotDrug-Target Network Visualization
enrichGO2GO Term Enrichment with Hypergeometric Test
enrichKEGG2KEGG Pathway Enrichment with Hypergeometric Test
enrichMOAMOA Category Enrichment with Hypergeometric Test
feaResultConstructor for 'feaResult-class'
feaResult-classfeaResult object
GCT-objectAn S4 Class to Represent a GCT Object
gctx2h5Convert GCTX to HDF5 File
gess_cmapCMAP Search Method
gess_corCorrelation-based Search Method
gess_fisherFisher Search Method
gess_gcmapgCMAP Search Method
gess_lincsLINCS Search Method
gessResultConstructor for 'gessResult-class'
gessResult-classgessResult object
gess_res_visGESS Result Visualization
getSigDrawn Query GES from Reference Database
get_targetsTarget Gene/Protein IDs for Query Drugs
gseGO2Modified GSEA with GO Terms
gseKEGG2Modified GSEA with KEGG
head-methodsReturn the First Part of an Object
mabsGOMeanAbs Enrichment Analysis for GO
mabsKEGGMeanAbs Enrichment Analysis for KEGG
matrix2h5Write Matrix to HDF5 file
moa_connSummarize GESS Results on MOA Level
parse_gctxParse GCTX
qSigHelper Function to Construct a 'qSig' Object
qSig-classClass "qSig"
rand_query_ESGenerate WTCS Null Distribution with Random Queries
result-methodsMethod to Extract Result Slots
show-methodsshow method
signatureSearch-packageEnvironment for Gene Expression Signature Searching Combined...
sim_score_grpSummary Scores by Groups of Cell Types
tail-methodsReturn the Last Part of an Object
targetListTarget Sample Data Set
tsea_dup_hyperGTarget Set Enrichment Analysis (TSEA) with Hypergeometric...
tsea_mabsTarget Set Enrichment Analysis (TSEA) with meanAbs
tsea_mGSEATarget Set Enrichment Analysis (TSEA) with mGSEA Algorithm
signatureSearch documentation built on April 8, 2020, 2 a.m.