Package: STdeconvolve
Type: Package
Title: Reference-free Cell-Type Deconvolution of Multi-Cellular
        Spatially Resolved Transcriptomics Data
Version: 1.4.0
Authors@R: 
    c(person(given = "Brendan",
           family = "Miller",
           role = c("aut", "cre"),
           email = "bmill3r@gmail.com",
           comment = c(ORCID = "0000-0002-9559-4045")),
           person(given = "Jean",
                  family = "Fan",
                  role = c("aut"),
                  email = "jeanfan@jhu.edu",
                  comment = c(ORCID = "0000-0002-0212-5451"))
    )
URL: https://jef.works/STdeconvolve/
BugReports: https://github.com/JEFworks-Lab/STdeconvolve/issues
Description: 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.
biocViews: Transcriptomics, Visualization, RNASeq, Bayesian, Spatial,
        Software, GeneExpression
License: GPL-3
Encoding: UTF-8
LazyData: FALSE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Imports: topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2,
        scatterpie, viridis, slam, stats, clue, liger, reshape2,
        graphics, grDevices, utils
Depends: R (>= 4.1)
Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots,
        gridExtra, hash, dplyr, parallel
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/STdeconvolve
git_branch: RELEASE_3_17
git_last_commit: 0f0d821
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
NeedsCompilation: no
Packaged: 2023-04-26 05:37:13 UTC; biocbuild
Author: Brendan Miller [aut, cre] (<https://orcid.org/0000-0002-9559-4045>),
  Jean Fan [aut] (<https://orcid.org/0000-0002-0212-5451>)
Maintainer: Brendan Miller <bmill3r@gmail.com>
Built: R 4.3.0; ; 2023-04-26 16:30:12 UTC; windows
