Package: OncoScore 1.41.0

Luca De Sano

OncoScore: A tool to identify potentially oncogenic genes

OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.

Authors:Luca De Sano [cre, aut], Carlo Gambacorti Passerini [ctb], Rocco Piazza [ctb], Daniele Ramazzotti [aut], Roberta Spinelli [ctb]

OncoScore_1.41.0.tar.gz
OncoScore_1.41.0.zip(r-4.7)OncoScore_1.41.0.zip(r-4.6)OncoScore_1.41.0.zip(r-4.5)
OncoScore_1.41.0.tgz(r-4.6-any)OncoScore_1.41.0.tgz(r-4.5-any)
OncoScore_1.41.0.tar.gz(r-4.7-any)OncoScore_1.41.0.tar.gz(r-4.6-any)
OncoScore_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
OncoScore/json (API)
NEWS

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

Bug tracker:https://github.com/danro9685/oncoscore/issues

Datasets:
  • genes - A list of genes
  • query - The result of perform.web.query on genes
  • query.timepoints - The result of perform.time.series.query on genes and timepoints
  • timepoints - A list of timepoints

On BioConductor:OncoScore-1.41.0(bioc 3.24)OncoScore-1.40.0(bioc 3.23)

biomedicalinformatics

6.15 score 5 stars 2 scripts 369 downloads 7 mentions 10 exports 56 dependencies

Last updated from:5f63256c88. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE160
linux-devel-x86_64OK219
source / vignettesOK285
linux-release-x86_64OK239
macos-release-arm64OK120
macos-oldrel-arm64OK122
windows-develOK154
windows-releaseOK144
windows-oldrelOK159
wasm-releaseOK134

Exports:combine.query.resultscompute.oncoscorecompute.oncoscore.from.regioncompute.oncoscore.timeseriesget.genes.from.biomartperform.queryperform.query.from.regionperform.query.timeseriesplot.oncoscoreplot.oncoscore.timeseries

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrxml2XVector

Introduction

Luca De Sano, Carlo Gambacorti Passerini, Rocco Piazza, Daniele Ramazzotti, Roberta Spinelli

Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon May 30 2026.

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

Running OncoScore

Luca De Sano, Carlo Gambacorti Passerini, Rocco Piazza, Daniele Ramazzotti, Roberta Spinelli

Rendered fromv2_running_OncoScore.Rmdusingknitr::rmarkdownon May 30 2026.

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

Readme and manuals

Help Manual

Help pageTopics
combine.query.resultscombine.query.results
combine.single.matrixcombine.single.matrix
compute.frequencies.scorescompute.frequencies.scores
compute.oncoscorecompute.oncoscore
compute.oncoscore.from.regioncompute.oncoscore.from.region
compute.oncoscore.timeseriescompute.oncoscore.timeseries
estimate.oncogenesestimate.oncogenes
A list of genesgenes
get.genes.from.biomartget.genes.from.biomart
get.list.from.xmlget.list.from.xml
get.pubmed.driver.analysisget.pubmed.driver.analysis
perform.queryperform.query
perform.query.from.regionperform.query.from.region
perform.query.timeseriesperform.query.timeseries
plot.oncoscoreplot.oncoscore
plot.oncoscore.timeseriesplot.oncoscore.timeseries
The result of perform.web.query on genesquery
The result of perform.time.series.query on genes and timepointsquery.timepoints
A list of timepointstimepoints
try.scantry.scan