Files in MikeDMorgan/miloR

Differential neighbourhood abundance testing on a graph

.Rbuildignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/RCMD_check.yml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/AllClasses.R R/AllGenerics.R R/RcppExports.R R/annotateNhoods.R R/buildFromAdjacency.R R/buildGraph.R R/buildNhoodGraph.R R/calcNhoodDistance.R R/calcNhoodExpression.R R/checkSeparation.R R/countCells.R R/findNhoodGroupMarkers.R R/findNhoodMarkers.R R/glmm.R R/graphSpatialFDR.R R/groupNhoods.R R/makeNhoods.R R/methods.R R/milo.R R/miloR-package.R R/miloR.R R/plotNhoods.R R/sim_discrete.R R/sim_family.R R/sim_nbglmm.R R/sim_trajectory.R R/testDiffExp.R R/testNhoods.R R/utils.R README.md

_pkgdown.yml

codecov.yml

data/sim_discrete.RData

data/sim_family.RData

data/sim_nbglmm.RData

data/sim_trajectory.RData

docs/404.html

docs/articles/index.html

docs/articles/milo_demo.html

docs/articles/milo_demo_files/accessible-code-block-0.0.1/empty-anchor.js

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docs/articles/milo_demo_files/header-attrs-2.3/header-attrs.js

docs/articles/milo_gastrulation.html

docs/articles/milo_gastrulation_files/accessible-code-block-0.0.1/empty-anchor.js

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docs/articles/milo_gastrulation_files/header-attrs-2.3/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/milo_schematic.png

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Milo.html

docs/reference/annotateNhoods.html

docs/reference/buildFromAdjacency.html

docs/reference/buildGraph.html

docs/reference/buildNhoodGraph.html

docs/reference/calcNhoodDistance.html

docs/reference/calcNhoodExpression.html

docs/reference/countCells.html

docs/reference/findNhoodMarkers.html

docs/reference/graphSpatialFDR.html

docs/reference/index.html

docs/reference/makeNhoods.html

docs/reference/matrixORMatrix-class.html

docs/reference/methods.html

docs/reference/plotDAbeeswarm.html

docs/reference/plotNhoodExpressionDA.html

docs/reference/plotNhoodGraph.html

docs/reference/plotNhoodGraphDA.html

docs/reference/plotNhoodSizeHist-1.png

docs/reference/plotNhoodSizeHist.html

docs/reference/sim_discrete.html

docs/reference/sim_trajectory.html

docs/reference/testDiffExp.html

docs/reference/testNhoods.html

man/Milo.Rd man/Satterthwaite_df.Rd man/annotateNhoods.Rd man/buildFromAdjacency.Rd man/buildGraph.Rd man/buildNhoodGraph.Rd man/calcNhoodDistance.Rd man/calcNhoodExpression.Rd man/checkSeparation.Rd man/computePvalue.Rd man/countCells.Rd man/findNhoodGroupMarkers.Rd man/findNhoodMarkers.Rd man/fitGLMM.Rd man/fitGeneticPLGlmm.Rd man/fitPLGlmm.Rd man/glmmControl.defaults.Rd man/graphSpatialFDR.Rd man/groupNhoods.Rd man/initialiseG.Rd man/initializeFullZ.Rd man/makeNhoods.Rd man/matrix.trace.Rd man/methods.Rd man/miloR-package.Rd man/miloR.Rd man/plotDAbeeswarm.Rd man/plotNhoodCounts.Rd man/plotNhoodExpressionDA.Rd man/plotNhoodGraph.Rd man/plotNhoodGraphDA.Rd man/plotNhoodGroups.Rd man/plotNhoodMA.Rd man/plotNhoodSizeHist.Rd man/sim_discrete.Rd man/sim_family.Rd man/sim_nbglmm.Rd man/sim_trajectory.Rd man/testDiffExp.Rd man/testNhoods.Rd miloR.R

miloR_sticker.png

milo_schematic.png

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/computeMatrices.cpp

src/computeMatrices.h

src/fitGeneticPLGlmm.cpp

src/fitPLGlmm.cpp

src/inference.cpp

src/inference.h

src/invertPseudoVar.cpp

src/invertPseudoVar.h

src/multiP.cpp

src/multiP.h

src/paramEst.cpp

src/paramEst.h

src/pseudovarPartial.cpp

src/pseudovarPartial.h

src/utils.cpp

src/utils.h

tests/testthat.R tests/testthat/test_annotateNhoods.R tests/testthat/test_buildFromAdjacency.R tests/testthat/test_buildGraph.R tests/testthat/test_buildNhoodGraph.R tests/testthat/test_calcNhoodDistance.R tests/testthat/test_calcNhoodExpression.R tests/testthat/test_checkSeparation.R tests/testthat/test_classes.R tests/testthat/test_countCells.R tests/testthat/test_findNhoodGroupMarkers.R tests/testthat/test_findNhoodMarkers.R tests/testthat/test_glmm.R tests/testthat/test_graphSpatialFDR.R tests/testthat/test_groupNhoodMarkers.R tests/testthat/test_makeNhoods.R tests/testthat/test_plotNhoods.R tests/testthat/test_testDiffExp.R tests/testthat/test_testNhoods.R

vignettes/.gitignore

vignettes/milo_contrasts.Rmd vignettes/milo_demo.Rmd vignettes/milo_gastrulation.Rmd vignettes/milo_glmm.Rmd

vignettes/milo_glmm.html

MikeDMorgan/miloR documentation built on Feb. 29, 2024, 6:20 p.m.