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>

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

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")

The TOAST User's Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software

Version 1.8.3

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

Suggests BiocStyle, knitr, rmarkdown, 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_1.8.3.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

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 3.14 Source Archive