STdeconvolve

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see STdeconvolve.

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

DOI: 10.18129/B9.bioc.STdeconvolve

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-9559-4045 , Jean Fan [aut] ORCID iD ORCID: 0000-0002-0212-5451

Maintainer: Brendan Miller <bmill3r at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, GeneExpression, RNASeq, Software, Spatial, Transcriptomics, Visualization

Version 1.12.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 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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Follow Installation instructions to use this package in your R session.

Source Package

Windows Binary (x86_64)

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Source Repository git clone https://git.bioconductor.org/packages/STdeconvolve

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/STdeconvolve

Package Short Url https://bioconductor.org/packages/STdeconvolve/

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