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Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


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
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Suggests nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray
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Follow Installation instructions to use this package in your R session.

Source Package lute_1.0.0.tar.gz
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