TOAST

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TOAST.

Tools for the analysis of heterogeneous tissues


Bioconductor version: 3.11

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. improve variable selection in reference-free deconvolution 3. partial reference-free deconvolution with prior knowledge.

Author: Ziyi Li and Hao Wu

Maintainer: Ziyi Li <ziyi.li at emory.edu>

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

Installation

To install this package, start R (version "4.0") 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")
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 1.2.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-2
Depends R (>= 3.6), RefFreeEWAS, EpiDISH, limma, nnls
Imports stats, methods, SummarizedExperiment
System Requirements
URL
Bug Reports https://github.com/ziyili20/TOAST/issues
See More
Suggests BiocStyle, knitr, rmarkdown, csSAM, gplots, matrixStats, Matrix
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 TOAST_1.2.0.tar.gz
Windows Binary TOAST_1.2.0.zip
macOS 10.13 (High Sierra) TOAST_1.2.0.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
Old Source Packages for BioC 3.11 Source Archive