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STROMA4

Assign Properties to TNBC Patients


Bioconductor version: Release (3.18)

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 mail.mcgill.ca>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("STROMA4")

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

Documentation

Reference Manual PDF

Details

biocViews BiomedicalInformatics, Classification, GeneExpression, ImmunoOncology, Microarray, RNASeq, Software
Version 1.26.0
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
Imports
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Suggests breastCancerMAINZ
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary STROMA4_1.26.0.zip (64-bit only)
macOS Binary (x86_64) STROMA4_1.26.0.tgz
macOS Binary (arm64) STROMA4_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/STROMA4
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/STROMA4
Bioc Package Browser https://code.bioconductor.org/browse/STROMA4/
Package Short Url https://bioconductor.org/packages/STROMA4/
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