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 is the development version of STdeconvolve; for the stable release version, see STdeconvolve.
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data
Bioconductor version: Development (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:
Maintainer: Brendan Miller <bmill3r at gmail.com>
citation("STdeconvolve")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("STdeconvolve")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Bayesian, GeneExpression, RNASeq, Software, Spatial, Transcriptomics, Visualization |
| Version | 1.11.1 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |