DESCRIPTION

Package: gpsFISH
Title: Optimization of Gene Panels for Targeted Spatial Transcriptomics
Version: 0.1.0
Authors@R: 
    person("Yida", "Zhang", , "yidazhang@ucla.edu", role = c("cre", "aut"))
Author: Yida Zhang [cre, aut]
Maintainer: Yida Zhang <yidazhang@ucla.edu>
Description: Methods for spatial transcriptomic analysis based on highly
    multiplexed single-molecule fluorescence in situ hybridization
    (hm-smFISH) hold particular promise in analysis of complex tissues.
    Most such methods, however, measure only a panel of genes, which need
    to be selected in advance to recognize cell types or processes
    relevant to the tissue being studied. Here, we develop GPS-FISH, a
    computational method that selects a panel of genes to optimize
    detection of previously annotated cell types or cell type hierarchies,
    based on scRNA-seq data. During the gene panel design, we account for
    platform effects between single cell RNA sequencing and spatial
    transcriptomics technologies. In addition, GPS-FISH can incorporate
    the hierarchical structure of cell types to account for complex cell
    type relationships. We also provide flexible options for other complex
    custom preferences.
License: MIT + file LICENSE
URL: https://github.com/kharchenkolab/gpsFISH
BugReports: https://github.com/kharchenkolab/gpsFISH/issues
Depends: 
    R (>= 3.5.0)
Imports: 
    bayesplot (>= 1.8.1),
    boot (>= 1.3-28),
    caret (>= 6.0.88),
    data.table (>= 1.14.0),
    deming (>= 1.4),
    e1071 (>= 1.7.8),
    ggplot2,
    ggpointdensity (>= 0.1.0),
    Matrix,
    naivebayes (>= 0.9.7),
    pagoda2 (>= 1.0.4),
    parallel,
    pROC (>= 1.17.0.1),
    ranger (>= 0.13.1),
    rstan (>= 2.21.2),
    splitTools (>= 0.3.1),
    viridis (>= 0.6.1)
Suggests: 
    cowplot (>= 1.1.1),
    dplyr (>= 1.0.7),
    ggdendro (>= 0.1.22),
    knitr,
    pheatmap (>= 1.0.12),
    reshape2 (>= 1.4.4),
    rmarkdown,
    Seurat (>= 4.0.3)
VignetteBuilder: 
    knitr
Encoding: UTF-8
LazyData: true
LazyDataCompression: bzip2
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3