Files in JEFworks/MERingue
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/MERingue-package.R
R/RcppExports.R
R/app.R
R/cluster.R
R/correlationStatistics.R
R/data.R
R/external.R
R/main.R
R/nearestNeighbor.R
R/parameterChoice.R
R/plot.R
R/process.R
R/tsm.R
README.md
data/BCL.rda
data/drosophila.rda
data/mOB.rda
data/mPOA.rda
data/mouseCoronal.rda
data/purkinje.rda
data/receptorLigandInfo.rda
docs/BCL_analysis.md
docs/BCL_analysis_files/figure-markdown_strict/bcl-clean-1.png
docs/BCL_analysis_files/figure-markdown_strict/bcl-inconsistent-1.png
docs/BCL_analysis_files/figure-markdown_strict/bcl-indsection-1.png
docs/BCL_analysis_files/figure-markdown_strict/bcl-init-1.png
docs/BCL_analysis_files/figure-markdown_strict/bcl-sample-1.png
docs/BCL_analysis_files/figure-markdown_strict/bcl-sample-2.png
docs/README.md
docs/_config.yml
docs/_layouts/default.html
docs/assets/css/style.scss
docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.eot
docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.svg
docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.ttf
docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.woff
docs/assets/fonts/Noto-Sans-700/Noto-Sans-700.woff2
docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.eot
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docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.ttf
docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.woff
docs/assets/fonts/Noto-Sans-700italic/Noto-Sans-700italic.woff2
docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.eot
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docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.ttf
docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.woff
docs/assets/fonts/Noto-Sans-italic/Noto-Sans-italic.woff2
docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.eot
docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.svg
docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.ttf
docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.woff
docs/assets/fonts/Noto-Sans-regular/Noto-Sans-regular.woff2
docs/assets/img/logo.png
docs/assets/img/meringue_overview.png
docs/assets/img/meringue_sample.png
docs/assets/js/scale.fix.js
docs/drosophila_3D_analysis.md
docs/drosophila_3D_analysis_files/figure-markdown_strict/drosophila-data-1.png
docs/drosophila_3D_analysis_files/figure-markdown_strict/drosophila-pattern-1.png
docs/drosophila_3D_analysis_files/figure-markdown_strict/drosophila-scc-1.png
docs/drosophila_3D_analysis_files/figure-markdown_strict/drosophila-sub-1.png
docs/favicon.ico
docs/img/meringue_logo.png
docs/index.md
docs/mOB_analysis.md
docs/mOB_analysis_files/figure-markdown_strict/mob-comparison-1.png
docs/mOB_analysis_files/figure-markdown_strict/mob-diff-gexp-plot-1.png
docs/mOB_analysis_files/figure-markdown_strict/mob-qc-1.png
docs/mOB_analysis_files/figure-markdown_strict/mob-spatial-heatmap-1.png
docs/mOB_analysis_files/figure-markdown_strict/mob-spatial-patterns2-1.png
docs/mOB_analysis_files/figure-markdown_strict/mob-spatially-cross-cor-1.png
docs/mOB_analysis_files/figure-markdown_strict/mob-spatially-unaware-1.png
docs/mOB_analysis_files/figure-markdown_strict/spatial-sub-network-1.png
docs/mOB_analysis_files/figure-markdown_strict/spatial-weights-1.png
docs/simulation.md
docs/simulation_files/figure-markdown_strict/s1-1.png
docs/simulation_files/figure-markdown_strict/s11-1.png
docs/simulation_files/figure-markdown_strict/s12-1.png
docs/simulation_files/figure-markdown_strict/s12-2.png
docs/simulation_files/figure-markdown_strict/s2-1.png
docs/simulation_files/figure-markdown_strict/s21-1.png
docs/simulation_files/figure-markdown_strict/s22-1.png
docs/simulation_files/figure-markdown_strict/s23-1.png
docs/simulation_files/figure-markdown_strict/s24-1.png
docs/simulation_files/figure-markdown_strict/s24-2.png
docs/simulation_files/figure-markdown_strict/s31-1.png
docs/simulation_files/figure-markdown_strict/s32-1.png
docs/simulation_files/figure-markdown_strict/s33-1.png
docs/simulation_files/figure-markdown_strict/sim-1.png
docs/spatial_clustering.md
docs/spatial_clustering_files/figure-markdown_strict/cluster-1.png
docs/spatial_clustering_files/figure-markdown_strict/cluster2-1.png
docs/spatial_clustering_files/figure-markdown_strict/simulation-pos-1.png
docs/spatial_clustering_files/figure-markdown_strict/simulation-trans-1.png
docs/spatial_clustering_files/figure-markdown_strict/simulation-trans2-1.png
docs/spatial_clustering_files/figure-markdown_strict/spatcluster-1.png
docs/spatial_clustering_files/figure-markdown_strict/spatcluster-2.png
docs/spatial_clustering_files/figure-markdown_strict/spatcluster-3.png
inst/CITATION
man/BCL.Rd
man/MERINGUE.Rd
man/cleanCounts.Rd
man/drosophila.Rd
man/filterSpatialPatterns.Rd
man/getBnn.Rd
man/getClusters.Rd
man/getCrossLayerNeighbors.Rd
man/getDifferentialGenes.Rd
man/getInterCellTypeWeight.Rd
man/getKnn.Rd
man/getMnn.Rd
man/getOverdispersedGenes.Rd
man/getPv.Rd
man/getSpatialNeighbors.Rd
man/getSpatialPatterns.Rd
man/getSpatiallyInformedClusters.Rd
man/groupSigSpatialPatterns.Rd
man/interCellTypeSpatialCrossCor.Rd
man/interpolate.Rd
man/lisaTest.Rd
man/mOB.Rd
man/mPOA.Rd
man/makeApp.Rd
man/moranPermutationTest.Rd
man/moranTest.Rd
man/moranTest_DEPRECATED.Rd
man/mouseCoronal.Rd
man/normalizeCounts.Rd
man/plotEmbedding.Rd
man/plotInterCellTypeSpatialCrossCor.Rd
man/plotNetwork.Rd
man/plotNetwork3D.Rd
man/purkinje.Rd
man/receptorLigandInfo.Rd
man/rotatePos.Rd
man/signedLisa.Rd
man/signedLisaPlot.Rd
man/spatialCrossCor.Rd
man/spatialCrossCorMatrix.Rd
man/spatialCrossCorTest.Rd
man/spatialCrossCorTorTest.Rd
man/winsorize.Rd
src/MERingue.so
src/Makevars.win
src/RcppExports.cpp
src/RcppExports.o
src/functions.cpp
src/functions.o
tests/testthat.R
tests/testthat/Rplots.pdf
tests/testthat/testCor.R
tests/testthat/testCpp.R
tests/testthat/testExt.R
tools/img/meringue_logo.svg
vignettes/BCL_analysis.Rmd
vignettes/drosophila_3D_analysis.Rmd
vignettes/mOB_analysis.Rmd
vignettes/mouseCoronal.Rmd
vignettes/simulation.Rmd
vignettes/spatial_clustering.Rmd
