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lute

This is the development version of lute; to use it, please install the devel version of Bioconductor.

Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments


Bioconductor version: Development (3.19)

Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.

Author: Sean K Maden [cre, aut] , Stephanie Hicks [aut]

Maintainer: Sean K Maden <maden.sean at gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("lute")

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("lute")
lute algorithm classes HTML R Script
Pseudobulk cell size rescaling example HTML R Script
The lute user's guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 0.99.27
In Bioconductor since BioC 3.19 (R-4.4)
License Artistic-2.0
Depends R (>= 4.3.0), stats, methods, utils, SummarizedExperiment, SingleCellExperiment, BiocGenerics
Imports S4Vectors, Biobase, scran, dplyr, ggplot2
System Requirements
URL https://github.com/metamaden/lute
Bug Reports https://github.com/metamaden/lute/issues
See More
Suggests nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray
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Package Archives

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

Source Package lute_0.99.27.tar.gz
Windows Binary lute_0.99.27.zip
macOS Binary (x86_64) lute_0.99.27.tgz
macOS Binary (arm64) lute_0.99.24.tgz
Source Repository git clone https://git.bioconductor.org/packages/lute
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lute
Bioc Package Browser https://code.bioconductor.org/browse/lute/
Package Short Url https://bioconductor.org/packages/lute/
Package Downloads Report Download Stats