TOAST
This is the development version of TOAST; for the stable release version, see TOAST.
Tools for the analysis of heterogeneous tissues
Bioconductor version: Development (3.21)
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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.21.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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 |
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_1.21.0.tar.gz |
| Windows Binary (x86_64) | TOAST_1.21.0.zip |
| macOS Binary (x86_64) | TOAST_1.21.0.tgz |
| macOS Binary (arm64) | TOAST_1.21.0.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 |