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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 (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews GeneExpression, Software, Survival
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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
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Suggests knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse
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Package Archives

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

Source Package TOP_1.3.0.tar.gz
Windows Binary TOP_1.3.0.zip
macOS Binary (x86_64) TOP_1.3.0.tgz
macOS Binary (arm64) TOP_1.3.0.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