Package: signatureSearch 1.21.0

Brendan Gongol

signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods.

Authors:Yuzhu Duan [aut], Brendan Gongol [cre, aut], Thomas Girke [aut]

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signatureSearch.pdf |signatureSearch.html✨
signatureSearch/json (API)
NEWS

# Install 'signatureSearch' in R:
install.packages('signatureSearch', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/yduan004/signaturesearch/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:signatureSearch-1.21.0(bioc 3.21)signatureSearch-1.20.0(bioc 3.20)

softwaregeneexpressiongokeggnetworkenrichmentsequencingcoveragedifferentialexpressioncpp

7.18 score 17 stars 1 packages 74 scripts 369 downloads 1 mentions 58 exports 163 dependencies

Last updated 2 months agofrom:eef2cb2fe4. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-win-x86_64NOTEDec 01 2024
R-4.5-linux-x86_64NOTEDec 01 2024
R-4.4-win-x86_64NOTEDec 01 2024
R-4.4-mac-x86_64NOTEDec 01 2024
R-4.4-mac-aarch64NOTEDec 01 2024
R-4.3-win-x86_64NOTEDec 01 2024
R-4.3-mac-x86_64NOTEDec 01 2024
R-4.3-mac-aarch64NOTEDec 01 2024

Exports:add_pcidaddGESSannotaddMOAappend2H5build_custom_dbcellNtestPlotcomp_fea_rescreate_empty_h5drug_cell_ranksdrugsdrugs<-dsea_GSEAdsea_hyperGdtnetplotenrichGO2enrichKEGG2enrichMOAenrichReactomefeaResultgctx2h5gess_cmapgess_corgess_fishergess_gcmapgess_lincsgess_res_visgessResultget_targetsgetDEGSiggetSiggetSPsubSiggetTreatsgmt2h5gseGO2gseKEGG2gseReactomelist_revlist2dfmabsGOmabsKEGGmabsReactomematrix2h5meanExpr2h5moa_connparse_gctxqSigrand_query_ESread_gmtresultrunWFset_readableshowsim_score_grptarReducetsea_dup_hyperGtsea_mabstsea_mGSEAvec_char_redu

Dependencies:abindannotateAnnotationDbiAnnotationHubapeaplotaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobbslibcachemclicliprclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestDOSEdplyrenrichplotevaluateExperimentHubfansifarverfastmapfastmatchfgseafilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgraphgridGraphicsGSEABasegsongtableHDF5ArrayhighrhmshtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplyrpngpolyclipprettyunitsprogresspurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreactome.dbreadrreshape2rhdf5rhdf5filtersRhdf5librlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesscatterpiesnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetinytextreeiotweenrtzdbUCSC.utilsutf8vctrsviridisLitevisNetworkvroomwithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc

signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Authors: Yuzhu Duan, Brendan Gongol, Dan S. Evans, Richard A. Miller, Nicholas J. Schork, Steven R. Cummings and Thomas Girke

Rendered fromsignatureSearch.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2023-04-05
Started: 2018-10-05

Readme and manuals

Help Manual

Help pageTopics
Environment for Gene Expression Signature Searching Combined with Functional Enrichment AnalysissignatureSearch-package signatureSearch
Add PCID to drug data frameadd_pcid
Add Compound Annotation Info to GESS Result TableaddGESSannot
Add MOA annotation to drug data frameaddMOA
Append Matrix to HDF5 Fileappend2H5
build_custom_dbbuild_custom_db
Calculates GSEA statistic valus for all gene sets in `selectedStats` list.calcGseaStatBatchCpp
LINCS 2017 Cell Type Informationcell_info
LINCS 2020 Cell Type Informationcell_info2
Number of Tests in Cell TypescellNtestPlot
MOA to Gene Mappingschembl_moa_list
MOA to Drug Name Mappingsclue_moa_list
Plot for Comparing Ranking Results of FEA Methodscomp_fea_res
Create Empty HDF5 Filecreate_empty_h5
Dimensions of an Objectdim dim,feaResult-method dim,gessResult-method
Summary ranking statistics across cell typesdrug_cell_ranks
Extract/Assign Drug Names for feaResultdrugs drugs,feaResult,ANY-method drugs,feaResult-method drugs<- drugs<-,feaResult-method
Drug Names Used in Examplesdrugs10
FEA Methodsdsea_GSEA dsea_hyperG tsea_dup_hyperG tsea_mabs tsea_mGSEA
Drug-Target Network Visualizationdtnetplot
GO Term Enrichment with Hypergeometric TestenrichGO2
KEGG Pathway Enrichment with Hypergeometric TestenrichKEGG2
MOA Category Enrichment with Hypergeometric TestenrichMOA
Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test.enrichReactome
Constructor for 'feaResult-class'feaResult
feaResult objectfeaResult-class
An S4 Class to Represent a GCT ObjectGCT object
Convert GCTX to HDF5 Filegctx2h5
GESS Methodsgess_cmap gess_cor gess_fisher gess_gcmap gess_lincs
GESS Result Visualizationgess_res_vis
Constructor for 'gessResult-class'gessResult
gessResult objectgessResult-class
Target Gene/Protein IDs for Query Drugsget_targets
getALLEGgetALLEG
getDbgetDb
Draw GESs from Reference DatabasegetDEGSig getSig getSPsubSig
Get Treatment InformationgetTreats
Convert GMT to HDF5 Filegmt2h5
Modified GSEA with GO TermsgseGO2
Modified GSEA with KEGGgseKEGG2
Modified GSEA with ReactomegseReactome
Return the First Part of an Objecthead head,feaResult-method head,gessResult-method
Instance Information of LINCS Expression Databaselincs_expr_inst_info
LINCS 2017 Perturbation Informationlincs_pert_info
LINCS 2020 Perturbation Informationlincs_pert_info2
LINCS Signature Informationlincs_sig_info
Reverse listlist_rev
Named list to data framelist2df
MeanAbs Enrichment Analysis for GOmabsGO
MeanAbs Enrichment Analysis for KEGGmabsKEGG
MeanAbs Enrichment Analysis for ReactomemabsReactome
Write Matrix to HDF5 filematrix2h5
Calculate Mean Expression Values of LINCS Level 3 DatameanExpr2h5
Summarize GESS Results on MOA Levelmoa_conn
Parse GCTXparse_gctx
Helper Function to Construct a 'qSig' ObjectqSig
Class "qSig"qSig-class
Generate WTCS Null Distribution with Random Queriesrand_query_ES
Read in gene set information from .gmt filesread_gmt
Method to Extract Result Slotsresult result,feaResult-method result,gessResult-method
Run the Entire GESS/FEA WorkflowrunWF
Set Readableset_readable
show methodshow show,feaResult-method show,gessResult-method show,qSig-method
Summary Scores by Groups of Cell Typessim_score_grp
Return the Last Part of an Objecttail tail,feaResult-method tail,gessResult-method
Target Sample Data SettargetList
Show Reduced TargetstarReduce
Reduce Number of Charactervec_char_redu