Package: toppgene 1.1.1

Pariksheet Nanda

toppgene: Gene List Enrichment Analysis using the ToppGene Suite

The ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. Although the ToppCluster web application provides convenient graphical access to the ToppGene Suite, the OpenAPI 3.0 compliant interface of ToppGene is better suited for automation and reproducibility. This package includes Bioconductor class interfaces and biological examples.

Authors:Pariksheet Nanda [aut, cre], Jason Shoemaker [fnd]

toppgene_1.1.1.tar.gz
toppgene_1.1.1.zip(r-4.7)toppgene_1.1.1.zip(r-4.6)toppgene_1.1.1.zip(r-4.5)
toppgene_1.1.1.tgz(r-4.6-any)toppgene_1.1.1.tgz(r-4.5-any)
toppgene_1.1.1.tar.gz(r-4.7-any)toppgene_1.1.1.tar.gz(r-4.6-any)
toppgene_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
toppgene/json (API)
NEWS

# Install 'toppgene' in R:

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

Bug tracker:https://github.com/immusystems-lab/toppgene/issues

On BioConductor:toppgene-1.1.0(bioc 3.24)toppgene-1.0.1(bioc 3.23)

clustering geneexpression genesetenrichment genetics motifdiscovery network networkenrichment pathways pharmacogenetics proteomics software thirdpartyclient

4.60 score 1 stars 2 scripts 42 downloads 8 exports 51 dependencies

Last updated from:1c21c29c82. Checks:1 NOTE, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	157
linux-devel-x86_64	ERROR	261
source / vignettes	OK	204
linux-release-x86_64	ERROR	242
macos-release-arm64	ERROR	173
macos-oldrel-arm64	ERROR	146
windows-devel	ERROR	148
windows-release	ERROR	140
windows-oldrel	ERROR	158
wasm-release	OK	114

Exports:CategoriesDataFrame default enrich lookup lookup_pubchem rownames<-show subset

Dependencies:askpass BiocFileCache BiocGenerics bit bit64 blob cachem cli clipr cpp11 crayon curl DBI dbplyr dplyr fastmap filelock generics glue hms httr2 IRanges jsonlite lifecycle magrittr memoise openssl pillar pkgconfig prettyunits progress purrr R6 rappdirs readr rlang RSQLite S4Vectors stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr xml2 yaml

Exporatory data analysis by querying the ToppGene Suite

Pariksheet Nanda

Rendered fromtoppgene.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-12-31
Started: 2024-12-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CategoriesDataFrame objects	CategoriesDataFrame CategoriesDataFrame-class default default,CategoriesDataFrame-method rownames<-,CategoriesDataFrame-method show,CategoriesDataFrame-method subset,CategoriesDataFrame-method [<-,CategoriesDataFrame-method [[<-,CategoriesDataFrame,ANY,ANY,ANY-method [[<-,CategoriesDataFrame-method
Return functional enrichment of gene Entrez IDs.	enrich
Return integer Entrez IDs from gene symbols, ensembl references, etc.	lookup
Return table of drug identifiers to PubChem CIDs.	lookup_pubchem
Convert identifiers of a single ToppGene drug database to PubChem CIDs.	lookup_pubchem_