TOAST
This is the released version of TOAST; for the devel version, see TOAST.
Tools for the analysis of heterogeneous tissues
Bioconductor version: Release (3.23)
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("TOAST")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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.
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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | TOAST_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | TOAST_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/TOAST/ |
| Package Short Url | https://bioconductor.org/packages/TOAST/ |
| Package Downloads Report | Download Stats |