Package: curatedBreastData 2.40.3

Levi Waldron

curatedBreastData: Curated breast cancer gene expression data with survival and treatment information

Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.

Authors:Katie Planey [aut], Levi Waldron [aut, cre]

curatedBreastData_2.40.3.tar.gz
curatedBreastData_2.40.3.tar.gz(r-4.7-any)curatedBreastData_2.40.3.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedBreastData/json (API)

# Install 'curatedBreastData' in R:

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

Bug tracker:https://github.com/waldronlab/curatedbreastdata/issues

Pkgdown/docs site:https://waldronlab.io

Datasets:

curatedBreastData_pData - CuratedBreastData_pData

On BioConductor:curatedBreastData-2.41.3(data/experiment 3.24)curatedBreastData-2.40.3(data/experiment 3.23)

experimentdata expressiondata cancerdata tissue breastcancerdata qpcrdata microarraydata geo tissuemicroarraydata bioconductor bioconductor-package itcr microarray transcriptomics u24ca289073 datapkg

5.24 score 6 scripts 8 exports 70 dependencies

Last updated from:cc1be0eaf5 (on RELEASE_3_23). Checks:1 NOTE, 3 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	119
linux-devel	OK	208
source / vignettes	OK	209
linux-release	OK	205

Exports:collapseDupProbes filterAndImputeSamples filterGenesByVariance getClinicalData getCuratedBreastDataExprSetList processExpressionSet processExpressionSetList removeDuplicatedPatients

Dependencies:askpass base64enc Biobase BiocFileCache BiocGenerics BiocManager BiocStyle bit bit64 blob bookdown bslib cachem cli cpp11 curl DBI dbplyr digest dplyr evaluate farver fastmap filelock fontawesome fs generics ggplot2 glue gtable highr htmltools httr2 impute isoband jquerylib jsonlite knitr labeling lifecycle magrittr memoise mime openssl pillar pkgconfig purrr R6 rappdirs RColorBrewer rlang rmarkdown RSQLite S7 sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML yaml

curatedBreastData Manual

Rendered fromcuratedBreastData-manual.Rmdusingknitr::rmarkdown

Last update: 2026-07-17
Started: 2026-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Collapse/handle duplicated probes (genes) in a dataset	collapseDupProbes
curatedBreastData_pData	curatedBreastData_pData
Filter and Impute Samples	filterAndImputeSamples
Filter genes by variance	filterGenesByVariance
Clinical Data Table & Variable Definitions	getClinicalData
getCuratedBreastDataExprSetList	getCuratedBreastDataExprSetList
Post-process a normalized assayData in an ExpressionSet object	processExpressionSet
Process a list of S4 expressionSet objects.	processExpressionSetList
Remove duplicated patient samples (samples from the same patient/column ID)	removeDuplicatedPatients