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5 | An R package for the visualization and analysis of spatially-resolved transcriptomics data,
6 | such as those generated with 10X Visium. The **spatialGE** package features a data object
7 | (STlist: Spatial Transctiptomics List) to store data and results from multiple tissue sections,
8 | as well as associated analytical methods for:
9 |
10 | - Visualization: `STplot`, `gene_interpolation`, `STplot_interpolation` to explore gene
11 | expression in spatial context.
12 | - Spatial autocorrelation: `SThet`, `compare_SThet` to assess the level of spatial uniformity in
13 | gene expression by calculating Moran's I and/or Geary's C and qualitatively explore correlations with
14 | sample-level metadata (i.e., tissue type, therapy, disease status).
15 | - Tissue domain/niche detection: `STclust` to perform spatially-informed hierarchical clustering for
16 | prediction of tissue domains in samples.
17 | - Gene set spatial enrichment: `STenrich` to detect gene sets with indications of spatial
18 | patterns (i.e., non-spatially uniform gene set expression).
19 | - Gene expression spatial gradients: `STgradient` to detect genes with evidence of variation in
20 | expression with respect to a tissue domain.
21 | - Spatially-informed differential expression: `STdiff` to test for differentially expressed
22 | genes using mixed models with spatial covariance structures to account of spatial dependency
23 | among spots/cells. It also supports non-spatial tests (Wilcoxon's and T-test).
24 |
25 | The methods in the initial spatialGE release, technical details, and their utility are presented in
26 | this publication: https://doi.org/10.1093/bioinformatics/btac145. For details on the recently
27 | developed methods `STenrich`, `STgradient`, and `STdiff` please refer to the spatialGE documentation.
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YEAR: 2023 63 | COPYRIGHT HOLDER: Moffitt Cancer Center 64 |65 | 66 |
Copyright (c) 2023 Moffitt Cancer Center
65 |Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
66 |The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
67 |THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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