TOAST

DOI: 10.18129/B9.bioc.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 (3.15)

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. improve variable selection in reference-free deconvolution 3. partial reference-free deconvolution with prior knowledge.

Author: Ziyi Li and Hao Wu

Maintainer: Ziyi Li <ziyi.li at emory.edu>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software
Version 1.9.0
In Bioconductor since BioC 3.10 (R-3.6) (2 years)
License GPL-2
Depends R (>= 3.6), RefFreeEWAS, EpiDISH, limma, nnls
Imports stats, methods, SummarizedExperiment, corpcor
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, csSAM, gplots, matrixStats, Matrix
SystemRequirements
Enhances
URL
BugReports https://github.com/ziyili20/TOAST/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/TOAST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TOAST
Package Short Url https://bioconductor.org/packages/TOAST/
Package Downloads Report Download Stats

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