STdeconvolve

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see STdeconvolve.

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

Bioconductor version: 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")):

Installation

To install this package, start R (version "4.3") and enter:


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

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("STdeconvolve")

STdeconvolve Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

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

Suggests knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel

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