STdeconvolve
This package is for version 3.15 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: 3.15
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>
citation("STdeconvolve")):
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")| STdeconvolve Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GeneExpression, RNASeq, Software, Spatial, Transcriptomics, Visualization |
| Version | 1.0.0 |
| 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 |
See More
| Suggests | knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/STdeconvolve/ |
| Package Short Url | https://bioconductor.org/packages/STdeconvolve/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |