STROMA4

DOI: 10.18129/B9.bioc.STROMA4  

Assign Properties to TNBC Patients

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("STROMA4")

 

PDF	R Script	Using the STROMA4 package
PDF		Reference Manual

Details

biocViews	BiomedicalInformatics, Classification, GeneExpression, ImmunoOncology, Microarray, RNASeq, Software
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	GPL-3
Depends	R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats, stats, graphics, utils
Imports
LinkingTo
Suggests	breastCancerMAINZ
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	STROMA4_1.22.0.tar.gz
Windows Binary	STROMA4_1.22.0.zip
macOS Binary (x86_64)	STROMA4_1.22.0.tgz
macOS Binary (arm64)	STROMA4_1.22.0.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/
Package Downloads Report	Download Stats