lute
This is the development version of lute; for the stable release version, see lute.
Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Sean K Maden <maden.sean at gmail.com>
citation("lute")):
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("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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lute_1.3.0.tar.gz |
| Windows Binary (x86_64) | lute_1.3.0.zip |
| macOS Binary (x86_64) | lute_1.3.0.tgz |
| macOS Binary (arm64) | |
| 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 |