Package: scToppR 1.0.0

Bryan Granger

scToppR: API Wrapper for ToppGene

scToppR provides an easy-to-use API wrapper for the ToppGene web platform, used for gene ontology and functional enrichment research. The package also integrates visualization tools, making it a convenient tool directly connecting ToppGene to code-based workflows in R. The tool can also easily save results into different formats.

Authors:Bryan Granger [aut, cre]

scToppR_1.0.0.tar.gz
scToppR_1.0.0.zip(r-4.7)scToppR_1.0.0.zip(r-4.6)scToppR_1.0.0.zip(r-4.5)
scToppR_1.0.0.tgz(r-4.6-any)scToppR_1.0.0.tgz(r-4.5-any)
scToppR_1.0.0.tar.gz(r-4.7-any)scToppR_1.0.0.tar.gz(r-4.6-any)
scToppR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scToppR/json (API)
NEWS

# Install 'scToppR' in R:

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

Bug tracker:https://github.com/bioinformaticsmusc/sctoppr/issues

Datasets:

ifnb.de - IFNB DE results
ifnb.markers.df - IFNB Marker DF
ifnb.markers.list.CD8T - IFNB Marker DF
pbmc.markers - PBMC markers
toppdata.airway - ToppData example using the airway dataset results
toppdata.ifnb - ToppData example for ifnb.de
toppdata.pbmc - ToppData example

On BioConductor:scToppR-1.1.0(bioc 3.24)scToppR-1.0.0(bioc 3.23)

pathways singlecell

5.92 score 7 stars 260 downloads 7 exports 40 dependencies

Last updated from:9569ca01eb (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	161
linux-devel-x86_64	WARNING	298
source / vignettes	OK	592
linux-release-x86_64	WARNING	331
macos-release-arm64	WARNING	165
macos-oldrel-arm64	WARNING	155
windows-devel	WARNING	217
windows-release	WARNING	222
windows-oldrel	WARNING	247
wasm-release	OK	146

Exports:addToppData get_Entrez get_ToppCats toppBalloon toppFun toppPlot toppSave

Dependencies:askpass cli cpp11 curl dplyr farver forcats generics ggplot2 glue gridExtra gtable httr2 isoband labeling lifecycle magrittr openssl openxlsx patchwork pillar pkgconfig R6 rappdirs RColorBrewer Rcpp rlang S7 scales stringi stringr sys tibble tidyselect utf8 vctrs viridis viridisLite withr zip

Introduction to scToppR

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-31
Started: 2023-12-19

scToppR with differential expression, Airway dataset

Rendered fromdifferential_expression_airway.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-31
Started: 2024-10-08

scToppR with differential expression, Seurat object data

Rendered fromdifferential_expression_seurat.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-31
Started: 2024-10-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add toppData results to SingleCellExperiment or SummarizedExperiment metadata	addToppData
Add toppData results to SingleCellExperiment or SummarizedExperiment metadata	addToppData
Convert genes into Entrez format	get_Entrez
Get a vector of ToppFun categories	get_ToppCats
IFNB DE results	ifnb.de
IFNB Marker DF	ifnb.markers.df
IFNB Marker DF	ifnb.markers.list.CD8T
PBMC markers	pbmc.markers
Create a balloon plot from toppdata results	toppBalloon
toppData example using the airway dataset results	toppdata.airway
toppData example for ifnb.de	toppdata.ifnb
toppData example	toppdata.pbmc
Get results from ToppFun	toppFun
Create a dotplot from toppdata results	toppPlot
Save toppData results (optionally) split by celltype/cluster	toppSave