Package: OncoScore 1.35.0

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_1.35.0.tar.gz
OncoScore_1.35.0.zip(r-4.5)OncoScore_1.35.0.zip(r-4.4)OncoScore_1.35.0.zip(r-4.3)
OncoScore_1.35.0.tgz(r-4.4-any)OncoScore_1.35.0.tgz(r-4.3-any)
OncoScore_1.35.0.tar.gz(r-4.5-noble)OncoScore_1.35.0.tar.gz(r-4.4-noble)
OncoScore_1.35.0.tgz(r-4.4-emscripten)OncoScore_1.35.0.tgz(r-4.3-emscripten)
OncoScore.pdf |OncoScore.html✨
OncoScore/json (API)
NEWS

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

Peer review:

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-1.33.1(bioc 3.20)OncoScore-1.32.0(bioc 3.19)

biomedicalinformatics

6.15 score 5 stars 2 scripts 236 downloads 7 mentions 10 exports 62 dependencies

Last updated 23 days agofrom:0ae7426685. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

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

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsrlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc

Introduction

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

Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon Oct 30 2024.

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 Oct 30 2024.

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