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Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

Bioconductor version: Release (3.18)

STdeconvolve as an unsupervised, reference-free approach to infer latent cell-type proportions and transcriptional profiles within multi-cellular spatially-resolved pixels from spatial transcriptomics (ST) datasets. STdeconvolve builds on latent Dirichlet allocation (LDA), a generative statistical model commonly used in natural language processing for discovering latent topics in collections of documents. In the context of natural language processing, given a count matrix of words in documents, LDA infers the distribution of words for each topic and the distribution of topics in each document. In the context of ST data, given a count matrix of gene expression in multi-cellular ST pixels, STdeconvolve applies LDA to infer the putative transcriptional profile for each cell-type and the proportional representation of each cell-type in each multi-cellular ST pixel.

Author: Brendan Miller [aut, cre] , Jean Fan [aut]

Maintainer: Brendan Miller <bmill3r at gmail.com>

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


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STdeconvolve Vignette HTML R Script
Reference Manual PDF


biocViews Bayesian, GeneExpression, RNASeq, Software, Spatial, Transcriptomics, Visualization
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.1)
Imports topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2, scatterpie, viridis, slam, stats, clue, liger, reshape2, graphics, grDevices, utils
System Requirements
URL https://jef.works/STdeconvolve/
Bug Reports https://github.com/JEFworks-Lab/STdeconvolve/issues
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Suggests knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel
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Source Package STdeconvolve_1.6.0.tar.gz
Windows Binary STdeconvolve_1.6.0.zip
macOS Binary (x86_64) STdeconvolve_1.6.0.tgz
macOS Binary (arm64) STdeconvolve_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/STdeconvolve
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/STdeconvolve
Bioc Package Browser https://code.bioconductor.org/browse/STdeconvolve/
Package Short Url https://bioconductor.org/packages/STdeconvolve/
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