cancerclass
This is the released version of cancerclass; for the devel version, see cancerclass.
Development and validation of diagnostic tests from high-dimensional molecular data
Bioconductor version: Release (3.23)
The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.
Author: Jan Budczies, Daniel Kosztyla
Maintainer: Daniel Kosztyla <danielkossi at hotmail.com>
citation("cancerclass")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cancerclass")
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("cancerclass")| Cancerclass: An R package for development and validation of diagnostic tests from high-dimensional molecular data | R Script | |
| Reference Manual |
Details
| biocViews | Cancer, Classification, Microarray, Software, Visualization |
| Version | 1.56.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 years) |
| License | GPL 3 |
| Depends | R (>= 2.14.0), Biobase, binom, methods, stats |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | cancerdata |
| 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 | cancerclass_1.56.0.tar.gz |
| Windows Binary (x86_64) | cancerclass_1.56.0.zip |
| macOS Binary (big-sur-x86_64) | cancerclass_1.56.0.tgz |
| macOS Binary (sonoma-arm64) | cancerclass_1.56.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cancerclass |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cancerclass |
| Bioc Package Browser | https://code.bioconductor.org/browse/cancerclass/ |
| Package Short Url | https://bioconductor.org/packages/cancerclass/ |
| Package Downloads Report | Download Stats |