Package: gep2pep 1.27.0

Francesco Napolitano

gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.

Authors:Francesco Napolitano <[email protected]>

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gep2pep.pdf |gep2pep.html✨
gep2pep/json (API)
NEWS

# Install 'gep2pep' in R:

install.packages('gep2pep', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:gep2pep-1.25.0(bioc 3.20)gep2pep-1.24.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression differentialexpression genesetenrichment dimensionreduction pathways go

4.48 score 4 scripts 193 downloads 3 mentions 25 exports 51 dependencies

Last updated 20 days agofrom:98fa3a0d6d. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:addSingleGeneSets as.CategorizedCollection buildPEPs CategorizedCollection checkRepository clearCache CondSEA createMergedRepository createRepository exportSEA gene2pathways getCollections getDetails getResults importFromRawMode importMSigDB.xml loadCollection loadESmatrix loadPVmatrix loadSampleGEP loadSamplePWS makeCollectionIDs openRepository PathSEA setId2setName

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI digest fastmap foreach GenomeInfoDb GenomeInfoDbData glue graph GSEABase httr IRanges iterators jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig plogr png R6 repo rhdf5 rhdf5filters Rhdf5lib rlang RSQLite S4Vectors sys UCSC.utils vctrs XML xtable XVector zlibbioc

Introduction to gep2pep

Francesco Napolitano

Rendered fromvignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2018-02-16
Started: 2017-09-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
gep2pep: creation and analysis of Pathway Expression Profiles	gep2pep-package gep2pep
Adds a collection of single-gene psuedo-sets.	addSingleGeneSets
Converts GeneSetCollection objects to CategorizedCollection objects.	as.CategorizedCollection
Build PEPs from GEPs and stores them in the repository.	buildPEPs
Constructor method for objects of class CategorizedCollection.	CategorizedCollection
A class to contain categorized gene set collection	CategorizedCollection-class
Check an existyng repository for consistency	checkRepository
Clear cached ranked matrices	clearCache
Performs Condition Set Enrichment Analysis	CondSEA
Merge multiple PEPs to build a repository of consensus PEPs	createMergedRepository
Creates a repository of pathway collections.	createRepository
Export CondSEA or PathSEA results to XLS format	exportSEA
Finds pathways including a given gene.	gene2pathways
Returns the names of the pathway collections in a repository.	getCollections
Extracts the details matrix from 'CondSEA' or 'PathSEA' output	getDetails
Extracts the results matrix from 'CondSEA' or 'PathSEA' output	getResults
Imports PEPs created in raw mode	importFromRawMode
Imports pathways data from an MSigDB XML file.	importMSigDB.xml
Loads a collection of pathways from the repository	loadCollection
Loads the matrix of Enrichment Scores for a collection	loadESmatrix
Loads the matrix of p-values for a collection	loadPVmatrix
Loads sample Gene Expression Profiles	loadSampleGEP
Loads sample pathway collections	loadSamplePWS
Creates a collection label for each pathway.	makeCollectionIDs
Opens an existing repository of pathway collections.	openRepository
Performs Pathway Set Enrichment Analysis (PSEA)	PathSEA
Converts gene set IDs to gene set names	setId2setName