Man pages for yduan004/signatureSearch
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

addGESSannotAdd Compound Annotation Info to GESS Result Table
addMOAAdd MOA annotation to drug data frame
add_pcidAdd PCID to drug data frame
append2H5Append Matrix to HDF5 File
build_custom_dbbuild_custom_db
calcGseaStatBatchCppCalculates GSEA statistic valus for all gene sets in...
cell_infoLINCS 2017 Cell Type Information
cell_info2LINCS 2020 Cell Type Information
cellNtestPlotNumber of Tests in Cell Types
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
dtnetplotDrug-Target Network Visualization
enrichGO2GO Term Enrichment with Hypergeometric Test
enrichKEGG2KEGG Pathway Enrichment with Hypergeometric Test
enrichMOAMOA Category Enrichment with Hypergeometric Test
enrichReactomeReactome Enrichment Analysis of a gene set. Given a vector of...
feaFEA Methods
feaResultConstructor for 'feaResult-class'
feaResult-classfeaResult object
GCT-objectAn S4 Class to Represent a GCT Object
gctx2h5Convert GCTX to HDF5 File
gessGESS Methods
gessResultConstructor for 'gessResult-class'
gessResult-classgessResult object
gess_res_visGESS Result Visualization
getALLEGgetALLEG
getDbgetDb
getSigDraw GESs from Reference Database
get_targetsTarget Gene/Protein IDs for Query Drugs
getTreatsGet Treatment Information
gmt2h5Convert GMT to HDF5 File
gseGO2Modified GSEA with GO Terms
gseKEGG2Modified GSEA with KEGG
gseReactomeModified GSEA with Reactome
head-methodsReturn the First Part of an Object
lincs_expr_inst_infoInstance Information of LINCS Expression Database
lincs_pert_infoLINCS 2017 Perturbation Information
lincs_pert_info2LINCS 2020 Perturbation Information
lincs_sig_infoLINCS Signature Information
list2dfNamed list to data frame
list_revReverse list
mabsGOMeanAbs Enrichment Analysis for GO
mabsKEGGMeanAbs Enrichment Analysis for KEGG
mabsReactomeMeanAbs Enrichment Analysis for Reactome
matrix2h5Write Matrix to HDF5 file
meanExpr2h5Calculate Mean Expression Values of LINCS Level 3 Data
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
read_gmtRead in gene set information from .gmt files
result-methodsMethod to Extract Result Slots
runWFRun the Entire GESS/FEA Workflow
set_readableSet Readable
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
tarReduceShow Reduced Targets
vec_char_reduReduce Number of Character
yduan004/signatureSearch documentation built on Feb. 19, 2024, 9:30 a.m.