Package: BreastSubtypeR 1.4.0

Qiao Yang

BreastSubtypeR: Cohort-aware methods for intrinsic molecular subtyping of breast cancer

BreastSubtypeR provides an assumption-aware, multi-method framework for intrinsic molecular subtyping of breast cancer. The package harmonizes several published nearest-centroid (NC) and single-sample predictor (SSP) classifiers, supplies method-specific preprocessing and robust probe-to-gene mapping, and implements a cohort-aware AUTO mode that selectively enables classifiers compatible with the cohort composition. A local Shiny app (iBreastSubtypeR) is included for interactive analyses and to support users without programming experience.

Authors:Qiao Yang [aut, cre], Emmanouil G. Sifakis [aut]

BreastSubtypeR_1.4.0.tar.gz
BreastSubtypeR_1.4.0.zip(r-4.7)BreastSubtypeR_1.4.0.zip(r-4.6)BreastSubtypeR_1.4.0.zip(r-4.5)
BreastSubtypeR_1.4.0.tgz(r-4.6-any)BreastSubtypeR_1.4.0.tgz(r-4.5-any)
BreastSubtypeR_1.4.0.tar.gz(r-4.7-any)BreastSubtypeR_1.4.0.tar.gz(r-4.6-any)
BreastSubtypeR_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BreastSubtypeR/json (API)
NEWS

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

Bug tracker:https://github.com/yqkiuo/breastsubtyper/issues

Datasets:

On BioConductor:BreastSubtypeR-1.5.0(bioc 3.24)BreastSubtypeR-1.4.0(bioc 3.23)

rnaseqsoftwaregeneexpressionclassificationpreprocessingvisualization

5.34 score 4 stars 11 scripts 254 downloads 15 exports 71 dependencies

Last updated from:f7156aeb58 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE167
linux-devel-x86_64OK342
source / vignettesOK272
linux-release-x86_64OK348
macos-release-arm64OK226
macos-oldrel-arm64OK220
windows-develOK297
windows-releaseOK253
windows-oldrelOK252
wasm-releaseOK165

Exports:BS_AIMSBS_cIHCBS_cIHC.itrBS_MultiBS_parkerBS_PCAPAM50BS_ssBCBS_sspbciBreastSubtypeRMappingVis_boxplotVis_heatmapVis_MultiVis_PCAVis_pie

Dependencies:abindBiobaseBiocGenericscirclizeclasscliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondata.tableDelayedArraydigestdoParalleldplyre1071edgeRfarverforeachgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtableimputeIRangesisobanditeratorslabelinglatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatspillarpkgconfigpngproxyR6RColorBrewerRcpprjsonrlangS4ArraysS4VectorsS7scalesSeqinfoshapeSparseArraystatmodstringistringrSummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector

BreastSubtypeR: Introduction and Workflow

Qiao Yang, Emmanouil G. Sifakis

Rendered fromBreastSubtypeR.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2025-11-23
Started: 2024-12-17