TOAST
This is the released version of TOAST; for the devel version, see TOAST.
All Bioconductor versions of TOAST
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10
Tools for the analysis of heterogeneous tissues
Bioconductor version: 3.23 · Package version: 1.26.0
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"):
Ziyi Li and Weiwei Zhang and Luxiao Chen and Hao Wu. TOAST: Tools for the analysis of heterogeneous tissues. doi:10.18129/B9.bioc.TOAST, R package version 1.26.0, https://bioconductor.org/packages/TOAST.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.26.0 |
| License | GPL-2 |
| Bug Reports | https://github.com/ziyili20/TOAST/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| Downloads rank | 313 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software |
| Package Short Url | https://bioconductor.org/packages/TOAST/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TOAST")| Analyses of high-throughput data from heterogeneous samples with TOAST | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | TOAST_1.26.0.tar.gz |
| Windows binary (x86_64) | TOAST_1.26.0.zip |
| macOS binary (arm64) | TOAST_1.26.0.tgz |
| macOS binary (x86_64) | TOAST_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TOAST |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TOAST |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog
Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally
Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
Reverse dependencies
Imports Me (3): cypress, MICSQTL, RegionalST