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'))

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-1.35.0(bioc 3.21)OncoScore-1.34.0(bioc 3.20)

biomedicalinformatics

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

Last updated 2 months agofrom:0ae7426685. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	OK	Nov 29 2024
R-4.5-linux	OK	Nov 29 2024
R-4.4-win	OK	Nov 29 2024
R-4.4-mac	OK	Nov 29 2024
R-4.3-win	OK	Nov 29 2024
R-4.3-mac	OK	Nov 29 2024

Exports:combine.query.results compute.oncoscore compute.oncoscore.from.region compute.oncoscore.timeseries get.genes.from.biomart perform.query perform.query.from.region perform.query.timeseries plot.oncoscore plot.oncoscore.timeseries

Dependencies:AnnotationDbi askpass Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr digest dplyr fansi fastmap filelock generics GenomeInfoDb GenomeInfoDbData glue hms httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs rlang RSQLite S4Vectors stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr xml2 XVector zlibbioc

Introduction

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

Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon Nov 29 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 Nov 29 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
combine.query.results	combine.query.results
combine.single.matrix	combine.single.matrix
compute.frequencies.scores	compute.frequencies.scores
compute.oncoscore	compute.oncoscore
compute.oncoscore.from.region	compute.oncoscore.from.region
compute.oncoscore.timeseries	compute.oncoscore.timeseries
estimate.oncogenes	estimate.oncogenes
A list of genes	genes
get.genes.from.biomart	get.genes.from.biomart
get.list.from.xml	get.list.from.xml
get.pubmed.driver.analysis	get.pubmed.driver.analysis
perform.query	perform.query
perform.query.from.region	perform.query.from.region
perform.query.timeseries	perform.query.timeseries
plot.oncoscore	plot.oncoscore
plot.oncoscore.timeseries	plot.oncoscore.timeseries
The result of perform.web.query on genes	query
The result of perform.time.series.query on genes and timepoints	query.timepoints
A list of timepoints	timepoints
try.scan	try.scan