Package: DESpace
Type: Package
Title: DESpace: a framework to discover spatially variable genes
Version: 1.0.0
Description: Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, 
  a popular method for performing differential expression analyses.
  Based on pre-annotated spatial clusters as summarized spatial information, 
  DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. 
  SVGs are then identified by testing the significance of spatial clusters. 
  The method is flexible and robust, and is faster than the most SV methods.
  Furthermore, to the best of our knowledge, it is the only SV approach that allows:
  - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability;
  - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.
Authors@R: c(
    person(given = "Peiying",
           family = "Cai",
           role = c("aut", "cre"),
           email = "peiying.cai@uzh.ch",
           comment = c(ORCID = "0009-0001-9229-2244")),
    person(given = "Simone",
           family = "Tiberi",
           role = c("aut", "cte"),
           email = "simone.tiberi@unibo.it",
           comment = c(ORCID = "0000-0002-3054-9964")))
biocViews: Spatial, SingleCell, RNASeq, Transcriptomics,
        GeneExpression, Sequencing,
        DifferentialExpression,StatisticalMethod, Visualization
License: GPL-3
Depends: R (>= 4.3.0)
Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment,
        ggplot2, ggpubr, scales, SummarizedExperiment, S4Vectors,
        BiocGenerics, data.table, assertthat, cowplot, ggforce,
        ggnewscale, patchwork, BiocParallel, methods
Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub,
        concaveman, spatialLIBD, purrr, scuttle, utils
VignetteBuilder: knitr
RoxygenNote: 7.2.3
ByteCompile: true
Encoding: UTF-8
URL: https://github.com/peicai/DESpace
BugReports: https://github.com/peicai/DESpace/issues
NeedsCompilation: no
Packaged: 2023-04-26 01:53:18 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/DESpace
git_branch: RELEASE_3_17
git_last_commit: 8a6b785
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Author: Peiying Cai [aut, cre] (<https://orcid.org/0009-0001-9229-2244>),
  Simone Tiberi [aut, cte] (<https://orcid.org/0000-0002-3054-9964>)
Maintainer: Peiying Cai <peiying.cai@uzh.ch>
Built: R 4.3.0; ; 2023-04-26 15:32:44 UTC; windows
