STdeconvolve

DOI: 10.18129/B9.bioc.STdeconvolve    

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

Bioconductor version: Release (3.15)

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 <bmille79 at jh.edu>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	STdeconvolve Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, GeneExpression, RNASeq, Software, Spatial, Transcriptomics, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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
LinkingTo
Suggests	knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel
SystemRequirements
Enhances
URL	https://jef.works/STdeconvolve/
BugReports	https://github.com/JEFworks-Lab/STdeconvolve/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	STdeconvolve_1.0.0.tar.gz
Windows Binary	STdeconvolve_1.0.0.zip
macOS Binary (x86_64)	STdeconvolve_1.0.0.tgz
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/
Package Downloads Report	Download Stats