TOAST

DOI: 10.18129/B9.bioc.TOAST    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see TOAST.

Tools for the analysis of heterogeneous tissues

Bioconductor version: 3.14

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. tree-based differential analysis 3. improve variable selection in reference-free deconvolution 4. partial reference-free deconvolution with prior knowledge.

Author: Ziyi Li and Weiwei Zhang and Luxiao Chen and Hao Wu

Maintainer: Ziyi Li <zli16 at mdanderson.org>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("TOAST")

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("TOAST")

 

HTML	R Script	The TOAST User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software
Version	1.8.3
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 years)
License	GPL-2
Depends	R (>= 3.6), EpiDISH, limma, nnls, quadprog
Imports	stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
SystemRequirements
Enhances
URL
BugReports	https://github.com/ziyili20/TOAST/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	TOAST_1.8.3.tar.gz
Windows Binary	TOAST_1.8.3.zip
macOS 10.13 (High Sierra)	TOAST_1.8.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TOAST
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TOAST
Package Short Url	https://bioconductor.org/packages/TOAST/
Package Downloads Report	Download Stats