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TOAST

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

Tools for the analysis of heterogeneous tissues


Bioconductor version: Development (3.19)

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>

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

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

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-2
Depends R (>= 3.6), EpiDISH, limma, nnls, quadprog
Imports stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally
System Requirements
URL
Bug Reports https://github.com/ziyili20/TOAST/issues
See More
Suggests BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
Linking To
Enhances
Depends On Me
Imports Me MICSQTL, RegionalST
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package TOAST_1.17.0.tar.gz
Windows Binary TOAST_1.17.0.zip
macOS Binary (x86_64) TOAST_1.17.0.tgz
macOS Binary (arm64) TOAST_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TOAST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TOAST
Bioc Package Browser https://code.bioconductor.org/browse/TOAST/
Package Short Url https://bioconductor.org/packages/TOAST/
Package Downloads Report Download Stats