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STROMA4

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

This is the development version of STROMA4; for the stable release version, see STROMA4.

Assign Properties to TNBC Patients


Bioconductor version: Development (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 mail.mcgill.ca>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.27.1
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
macOS Binary (x86_64) STROMA4_1.27.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/STROMA4
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/STROMA4
Package Short Url https://bioconductor.org/packages/STROMA4/
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