DESCRIPTION

Package: DSPWorkflow
Title: A Workflow for Analyzing Digital Spatial Profiling RNA Data
Version: 1.3.1
Authors@R: c(person("Rui", "He", email = "rui.he@nih.gov", role = "aut"), 
    person("Maggie", "Cam", email = "maggie.cam@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-8190-9766")), 
    person("Ned", "Cauley", email = "ned.cauley@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8968-6621")), 
    person("Jing", "Bian", email = "bianjh@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-7109-716X")), 
    person("Difei", "Wang", email = "difei.wang2@nih.gov", role = "aut", comment = c(ORCID = "0000-0003-4088-3859")),
    person("Chad", "Highfill", email = "chad.highfill@nih.gov", role = "aut", comment = c(ORCID = "0000-0003-0046-3593")),
    person("Aleksandra", "Michalowski", email = "michaloa@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-9259-6101")))
Description: A set of functions for analyzing RNA data from the spatial 
    transcriptomics approach Digital Spatial Profiling (Nanostring). The user 
    provides read count data and annotations, and the package outputs 
    normalized differential expression of genes and further visualizations and 
    analysis based on user input. It can be run in a docker container and in 
    user-friendly web-based interactive notebooks (NIDAP, Palantir Foundry).
URL: https://github.com/NIDAP-Community/DSPWorkflow
BugReports: https://github.com/NIDAP-Community/DSPWorkflow/issues
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews:
Suggests: 
    testthat (>= 3.1.4)
Depends:
    R (>= 4.1.3)
Imports:
    Biobase (>= 2.54.0),
    BiocGenerics (>= 0.40.0),
    cowplot (>= 1.1.1),
    dplyr (>= 1.0.9),
    GeomxTools (>= 3.1.1),
    ggforce (>= 0.3.4),
    ggplot2 (>= 3.3.6),
    gridExtra (>= 2.3),
    grid (>= 4.1.3),
    gtable (>= 0.3.0),
    knitr (>= 1.40),
    NanoStringNCTools (>= 1.2.0),
    patchwork (>= 1.1.2),
    reshape2 (>= 1.4.4),
    Rtsne (>= 0.16),
    scales (>= 1.2.1),
    stats (>= 4.1.3),
    SpatialDecon (>= 1.4.3),
    tibble (>= 3.1.8),
    tidyr (>= 1.2.1),
    umap (>= 0.2.9.0),
    magrittr (>= 2.0.3),
    ComplexHeatmap (>= 2.10.0)
Config/testthat/edition: 3