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

Tools for the analysis of heterogeneous tissues

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software
Version 1.19.0
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
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Suggests BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
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Imports Me MICSQTL, RegionalST
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Follow Installation instructions to use this package in your R session.

Source Package TOAST_1.19.0.tar.gz
Windows Binary
macOS Binary (x86_64) TOAST_1.19.0.tgz
macOS Binary (arm64) TOAST_1.19.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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