DESpace/DESCRIPTION at main · peicai/DESpace · GitHub

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Package: DESpace
Type: Package
Title: DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
Version: 2.3.2
Description: Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions 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.
  For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates.
  DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.
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"),
           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 (>= 4.5.0)
Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2,
        SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat,
        terra, sf, spatstat.explore, spatstat.geom, ggforce, ggnewscale,
        patchwork, BiocParallel, methods, scales, scuttle
Suggests: knitr, rmarkdown, testthat, BiocStyle, muSpaData, ExperimentHub,
        spatialLIBD, purrr, reshape2, tidyverse, concaveman
VignetteBuilder: knitr
RoxygenNote: 7.3.3
ByteCompile: true
Encoding: UTF-8
URL: https://github.com/peicai/DESpace, https://peicai.github.io/DESpace/
BugReports: https://github.com/peicai/DESpace/issues