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This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Assign Properties to TNBC Patients

Bioconductor version: Release (3.19)

This package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients. These four stromal properties were identified in Triple negative breast cancer (TNBC) patients and represent the presence of different cells in the stroma: T-cells (T), B-cells (B), stromal infiltrating epithelial cells (E), and desmoplasia (D). Additionally this package can also be used to estimate generative properties for the Lehmann subtypes, an alternative TNBC subtyping scheme (PMID: 21633166).

Author: Sadiq Saleh [aut, cre], Michael Hallett [aut]

Maintainer: Sadiq Saleh <sadiq.mehdiismailsaleh at>

Citation (from within R, enter citation("STROMA4")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews BiomedicalInformatics, Classification, GeneExpression, ImmunoOncology, Microarray, RNASeq, Software
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats, stats, graphics, utils
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