TOP

DOI: 10.18129/B9.bioc.TOP  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see TOP.

TOP Constructs Transferable Model Across Gene Expression Platforms

Bioconductor version: 3.17

TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

Author: Harry Robertson [aut, cre] , Nicholas Robertson [aut]

Maintainer: Harry Robertson <harry.robertson at sydney.edu.au>

Installation

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

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

BiocManager::install("TOP")

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("TOP")

 

HTML	R Script	Introduction to TOP
PDF		Reference Manual

Details

biocViews	GeneExpression, Software, Survival
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse
SystemRequirements
Enhances
URL	https://github.com/Harry25R/TOP
BugReports	https://github.com/Harry25R/TOP/issues
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	TOP_1.0.0.tar.gz
Windows Binary	TOP_1.0.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	TOP_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TOP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TOP
Bioc Package Browser	https://code.bioconductor.org/browse/TOP/
Package Short Url	https://bioconductor.org/packages/TOP/
Package Downloads Report	Download Stats