lute

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see lute.

Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Version 1.0.0

In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)

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

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_1.0.0.tar.gz

Windows Binary (x86_64) lute_1.0.0.zip

macOS Binary (x86_64) lute_1.0.0.tgz

macOS Binary (arm64) lute_1.0.0.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/

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