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]

# Install 'signatureSearch' in R:

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

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cell_info - LINCS 2017 Cell Type Information
cell_info2 - LINCS 2020 Cell Type Information
chembl_moa_list - MOA to Gene Mappings
clue_moa_list - MOA to Drug Name Mappings
drugs10 - Drug Names Used in Examples
lincs_expr_inst_info - Instance Information of LINCS Expression Database
lincs_pert_info - LINCS 2017 Perturbation Information
lincs_pert_info2 - LINCS 2020 Perturbation Information
lincs_sig_info - LINCS Signature Information
targetList - Target Sample Data Set

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

software geneexpression go kegg networkenrichment sequencing coverage differentialexpression

6.17 score 17 stars 1 packages 73 scripts 369 downloads 1 mentions 58 exports 163 dependencies

Last updated 23 days agofrom:eef2cb2fe4. Checks:ERROR: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 01 2024
R-4.5-win-x86_64	ERROR	Nov 01 2024
R-4.5-linux-x86_64	ERROR	Nov 01 2024
R-4.4-win-x86_64	ERROR	Nov 01 2024
R-4.4-mac-x86_64	ERROR	Nov 01 2024
R-4.4-mac-aarch64	ERROR	Nov 01 2024
R-4.3-win-x86_64	ERROR	Nov 01 2024
R-4.3-mac-x86_64	ERROR	Nov 01 2024
R-4.3-mac-aarch64	ERROR	Nov 01 2024

Exports:add_pcid addGESSannot addMOA append2H5 build_custom_db cellNtestPlot comp_fea_res create_empty_h5 drug_cell_ranks drugs drugs<-dsea_GSEA dsea_hyperG dtnetplot enrichGO2 enrichKEGG2 enrichMOA enrichReactome feaResult gctx2h5 gess_cmap gess_cor gess_fisher gess_gcmap gess_lincs gess_res_vis gessResult get_targets getDEGSig getSig getSPsubSig getTreats gmt2h5 gseGO2 gseKEGG2 gseReactome list_rev list2df mabsGO mabsKEGG mabsReactome matrix2h5 meanExpr2h5 moa_conn parse_gctx qSig rand_query_ES read_gmt result runWF set_readable show sim_score_grp tarReduce tsea_dup_hyperG tsea_mabs tsea_mGSEA vec_char_redu

Dependencies:abind annotate AnnotationDbi AnnotationHub ape aplot askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob bslib cachem cli clipr clusterProfiler codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray digest DOSE dplyr enrichplot evaluate ExperimentHub fansi farver fastmap fastmatch fgsea filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggfun ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim graph gridGraphics GSEABase gson gtable HDF5Array highr hms htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plyr png polyclip prettyunits progress purrr qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen reactome.db readr reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales scatterpie snow SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidyr tidyselect tidytree tinytex treeio tweenr tzdb UCSC.utils utf8 vctrs viridisLite visNetwork vroom withr xfun XML xtable XVector yaml yulab.utils zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis	signatureSearch-package signatureSearch
Add PCID to drug data frame	add_pcid
Add Compound Annotation Info to GESS Result Table	addGESSannot
Add MOA annotation to drug data frame	addMOA
Append Matrix to HDF5 File	append2H5
build_custom_db	build_custom_db
Calculates GSEA statistic valus for all gene sets in `selectedStats` list.	calcGseaStatBatchCpp
LINCS 2017 Cell Type Information	cell_info
LINCS 2020 Cell Type Information	cell_info2
Number of Tests in Cell Types	cellNtestPlot
MOA to Gene Mappings	chembl_moa_list
MOA to Drug Name Mappings	clue_moa_list
Plot for Comparing Ranking Results of FEA Methods	comp_fea_res
Create Empty HDF5 File	create_empty_h5
Dimensions of an Object	dim dim,feaResult-method dim,gessResult-method
Summary ranking statistics across cell types	drug_cell_ranks
Extract/Assign Drug Names for feaResult	drugs drugs,feaResult,ANY-method drugs,feaResult-method drugs<- drugs<-,feaResult-method
Drug Names Used in Examples	drugs10
FEA Methods	dsea_GSEA dsea_hyperG tsea_dup_hyperG tsea_mabs tsea_mGSEA
Drug-Target Network Visualization	dtnetplot
GO Term Enrichment with Hypergeometric Test	enrichGO2
KEGG Pathway Enrichment with Hypergeometric Test	enrichKEGG2
MOA Category Enrichment with Hypergeometric Test	enrichMOA
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 object	feaResult-class
An S4 Class to Represent a GCT Object	GCT object
Convert GCTX to HDF5 File	gctx2h5
GESS Methods	gess_cmap gess_cor gess_fisher gess_gcmap gess_lincs
GESS Result Visualization	gess_res_vis
Constructor for 'gessResult-class'	gessResult
gessResult object	gessResult-class
Target Gene/Protein IDs for Query Drugs	get_targets
getALLEG	getALLEG
getDb	getDb
Draw GESs from Reference Database	getDEGSig getSig getSPsubSig
Get Treatment Information	getTreats
Convert GMT to HDF5 File	gmt2h5
Modified GSEA with GO Terms	gseGO2
Modified GSEA with KEGG	gseKEGG2
Modified GSEA with Reactome	gseReactome
Return the First Part of an Object	head head,feaResult-method head,gessResult-method
Instance Information of LINCS Expression Database	lincs_expr_inst_info
LINCS 2017 Perturbation Information	lincs_pert_info
LINCS 2020 Perturbation Information	lincs_pert_info2
LINCS Signature Information	lincs_sig_info
Reverse list	list_rev
Named list to data frame	list2df
MeanAbs Enrichment Analysis for GO	mabsGO
MeanAbs Enrichment Analysis for KEGG	mabsKEGG
MeanAbs Enrichment Analysis for Reactome	mabsReactome
Write Matrix to HDF5 file	matrix2h5
Calculate Mean Expression Values of LINCS Level 3 Data	meanExpr2h5
Summarize GESS Results on MOA Level	moa_conn
Parse GCTX	parse_gctx
Helper Function to Construct a 'qSig' Object	qSig
Class "qSig"	qSig-class
Generate WTCS Null Distribution with Random Queries	rand_query_ES
Read in gene set information from .gmt files	read_gmt
Method to Extract Result Slots	result result,feaResult-method result,gessResult-method
Run the Entire GESS/FEA Workflow	runWF
Set Readable	set_readable
show method	show show,feaResult-method show,gessResult-method show,qSig-method
Summary Scores by Groups of Cell Types	sim_score_grp
Return the Last Part of an Object	tail tail,feaResult-method tail,gessResult-method
Target Sample Data Set	targetList
Show Reduced Targets	tarReduce
Reduce Number of Character	vec_char_redu