TOP
This is the development version of TOP; for the stable release version, see TOP.
TOP Constructs Transferable Model Across Gene Expression Platforms
DOI: 10.18129/B9.bioc.TOP
Bioconductor version: Development (3.20)
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("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 |
Details
| biocViews | GeneExpression, Software, Survival |
| Version | 1.5.0 |
| 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 |
See More
| 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_1.5.0.tar.gz |
| Windows Binary (x86_64) | TOP_1.5.0.zip |
| macOS Binary (x86_64) | TOP_1.5.0.tgz |
| macOS Binary (arm64) | TOP_1.5.0.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 |