TOP

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

TOP Constructs Transferable Model Across Gene Expression Platforms

Bioconductor version: Development (3.21)

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] (ORCID: ), Nicholas Robertson [aut]

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

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

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")

Introduction to TOP	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, Software, Survival
Version	1.7.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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
System Requirements
URL	https://github.com/Harry25R/TOP
Bug Reports	https://github.com/Harry25R/TOP/issues

Suggests	knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse
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	TOP_1.7.0.tar.gz
Windows Binary (x86_64)	TOP_1.7.0.zip
macOS Binary (x86_64)	TOP_1.7.0.tgz
macOS Binary (arm64)	TOP_1.7.0.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