STROMA4
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see STROMA4.
Assign Properties to TNBC Patients
Bioconductor version: 3.9
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("STROMA4")):
Installation
To install this package, start R (version "3.6") 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")| Using the STROMA4 package | R Script | |
| Reference Manual |
Details
| biocViews | BiomedicalInformatics, Classification, GeneExpression, ImmunoOncology, Microarray, RNASeq, Software |
| Version | 1.8.0 |
| 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 | |
| System Requirements | |
| URL |
See More
| Suggests | breastCancerMAINZ |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | STROMA4_1.8.0.tar.gz |
| Windows Binary | STROMA4_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | STROMA4_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/STROMA4 |
| Source Repository (Developer Access) | git clone [email protected]:packages/STROMA4 |
| Bioc Package Browser | https://code.bioconductor.org/browse/STROMA4/ |
| Package Short Url | https://bioconductor.org/packages/STROMA4/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |