├── .Rbuildignore ├── .gitattributes ├── .github └── workflows │ └── main.yml ├── .gitignore ├── .lintr ├── DESCRIPTION ├── FAQs.md ├── InSituType.Rproj ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── chooseClusterNumber.R ├── colorCellTypes.R ├── data.R ├── fastCohorting.R ├── find_anchor_cells.R ├── flightpath_layout.R ├── gen_profiles_protein.R ├── geoSketch.R ├── getProfiles.R ├── getSpatialContext.R ├── insitutype.R ├── insitutypeML.R ├── nbclust.R ├── refineClusters.R ├── rescaleProfiles.R ├── spatialUpdate.R └── utilities.R ├── README.md ├── azure-pipelines.yml ├── data ├── human_signature.RData ├── iocolors.RData ├── ioprofiles.RData ├── mini_nsclc.RData ├── mouse_signature.RData ├── tonsil_annotation.RData ├── tonsil_protein.RData └── tonsil_reference_profile.RData ├── man ├── Estep.Rd ├── Mstep.Rd ├── alignGenes.Rd ├── chooseClusterNumber.Rd ├── choose_anchors_from_stats.Rd ├── colorCellTypes.Rd ├── estimateBackground.Rd ├── estimatePlatformEffects.Rd ├── fastCohorting.Rd ├── find_anchor_cells.Rd ├── flightpath_layout.Rd ├── flightpath_plot.Rd ├── gen_profiles_protein_annotation.Rd ├── gen_profiles_protein_expression.Rd ├── geoSketch.Rd ├── geoSketch_get_plaid.Rd ├── geoSketch_sample_from_plaids.Rd ├── getMeanClusterConfidence.Rd ├── getProteinParameters.Rd ├── getRNAprofiles.Rd ├── getSpatialContext.Rd ├── get_anchor_stats.Rd ├── get_neighborhood_expression.Rd ├── human_signature.Rd ├── insitutype.Rd ├── insitutypeML.Rd ├── iocolors.Rd ├── ioprofiles.Rd ├── ismax.Rd ├── lldist.Rd ├── lls_protein.Rd ├── lls_rna.Rd ├── logliks2probs.Rd ├── mini_nsclc.Rd ├── mouse_signature.Rd ├── nbclust.Rd ├── nearestNeighborGraph.Rd ├── neighbor_colMeans.Rd ├── neighbor_colSums.Rd ├── numCores.Rd ├── prepDataForSketching.Rd ├── probs2logliks.Rd ├── radiusBasedGraph.Rd ├── refineAnchors.Rd ├── refineClusters.Rd ├── spatialUpdate.Rd ├── tonsil_annotation.Rd ├── tonsil_protein.Rd ├── tonsil_reference_profile.Rd ├── updateProfilesFromAnchors.Rd ├── updateReferenceProfiles.Rd └── update_logliks_with_cohort_freqs.Rd ├── reqs.md ├── specs.md ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp └── rcpparma_dnbinom_sparse.cpp ├── tests ├── testthat.R └── testthat │ ├── test-colorCellTypes.R │ ├── test_RCppExports.R │ ├── test_flightpath.R │ ├── test_getProfiles.R │ ├── test_getSpatialContext.R │ ├── test_insitutype_Protein.R │ ├── test_insitutype_RNA.R │ ├── test_refinecells_cell_merging_logic.R │ └── test_spatialUpdate.R └── vignettes ├── NSCLC-RNA_InsituType-vignette.Rmd ├── NSCLC-RNA_InsituType-vignette.html ├── NSCLC-clustering-SingleCellExperiment-vignette.Rmd ├── NSCLC-clustering-SingleCellExperiment-vignette.html ├── NSCLC-clustering-vignette.Rmd ├── NSCLC-clustering-vignette.html ├── NSCLC-semi-supervised-cell-typing-vignette.Rmd ├── NSCLC-semi-supervised-cell-typing-vignette.html ├── NSCLC-supervised-cell-typing-vignette.Rmd ├── NSCLC-supervised-cell-typing-vignette.html ├── TONSIL_Protein_Insitu_Cell_Typing-vignette.Rmd └── TONSIL_Protein_Insitu_Cell_Typing-vignette.html /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/.github/workflows/main.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/.gitignore -------------------------------------------------------------------------------- /.lintr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/.lintr -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /FAQs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/FAQs.md -------------------------------------------------------------------------------- /InSituType.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/InSituType.Rproj -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/RcppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/RcppExports.R -------------------------------------------------------------------------------- /R/chooseClusterNumber.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/chooseClusterNumber.R -------------------------------------------------------------------------------- /R/colorCellTypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/colorCellTypes.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/data.R -------------------------------------------------------------------------------- /R/fastCohorting.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/fastCohorting.R -------------------------------------------------------------------------------- /R/find_anchor_cells.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/find_anchor_cells.R -------------------------------------------------------------------------------- /R/flightpath_layout.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/flightpath_layout.R -------------------------------------------------------------------------------- /R/gen_profiles_protein.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/gen_profiles_protein.R -------------------------------------------------------------------------------- /R/geoSketch.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/geoSketch.R -------------------------------------------------------------------------------- /R/getProfiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/getProfiles.R -------------------------------------------------------------------------------- /R/getSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/getSpatialContext.R -------------------------------------------------------------------------------- /R/insitutype.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/insitutype.R -------------------------------------------------------------------------------- /R/insitutypeML.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/insitutypeML.R -------------------------------------------------------------------------------- /R/nbclust.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/nbclust.R -------------------------------------------------------------------------------- /R/refineClusters.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/refineClusters.R -------------------------------------------------------------------------------- /R/rescaleProfiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/rescaleProfiles.R -------------------------------------------------------------------------------- /R/spatialUpdate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/spatialUpdate.R -------------------------------------------------------------------------------- /R/utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/R/utilities.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/README.md -------------------------------------------------------------------------------- /azure-pipelines.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/azure-pipelines.yml -------------------------------------------------------------------------------- /data/human_signature.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/human_signature.RData -------------------------------------------------------------------------------- /data/iocolors.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/iocolors.RData -------------------------------------------------------------------------------- /data/ioprofiles.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/ioprofiles.RData -------------------------------------------------------------------------------- /data/mini_nsclc.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/mini_nsclc.RData -------------------------------------------------------------------------------- /data/mouse_signature.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/mouse_signature.RData -------------------------------------------------------------------------------- /data/tonsil_annotation.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/tonsil_annotation.RData -------------------------------------------------------------------------------- /data/tonsil_protein.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/tonsil_protein.RData -------------------------------------------------------------------------------- /data/tonsil_reference_profile.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/data/tonsil_reference_profile.RData -------------------------------------------------------------------------------- /man/Estep.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/Estep.Rd -------------------------------------------------------------------------------- /man/Mstep.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/Mstep.Rd -------------------------------------------------------------------------------- /man/alignGenes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/alignGenes.Rd -------------------------------------------------------------------------------- /man/chooseClusterNumber.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/chooseClusterNumber.Rd -------------------------------------------------------------------------------- /man/choose_anchors_from_stats.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/choose_anchors_from_stats.Rd -------------------------------------------------------------------------------- /man/colorCellTypes.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/colorCellTypes.Rd -------------------------------------------------------------------------------- /man/estimateBackground.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/estimateBackground.Rd -------------------------------------------------------------------------------- /man/estimatePlatformEffects.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/estimatePlatformEffects.Rd -------------------------------------------------------------------------------- /man/fastCohorting.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/fastCohorting.Rd -------------------------------------------------------------------------------- /man/find_anchor_cells.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/find_anchor_cells.Rd -------------------------------------------------------------------------------- /man/flightpath_layout.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/flightpath_layout.Rd -------------------------------------------------------------------------------- /man/flightpath_plot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/flightpath_plot.Rd -------------------------------------------------------------------------------- /man/gen_profiles_protein_annotation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/gen_profiles_protein_annotation.Rd -------------------------------------------------------------------------------- /man/gen_profiles_protein_expression.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/gen_profiles_protein_expression.Rd -------------------------------------------------------------------------------- /man/geoSketch.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/geoSketch.Rd -------------------------------------------------------------------------------- /man/geoSketch_get_plaid.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/geoSketch_get_plaid.Rd -------------------------------------------------------------------------------- /man/geoSketch_sample_from_plaids.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/geoSketch_sample_from_plaids.Rd -------------------------------------------------------------------------------- /man/getMeanClusterConfidence.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/getMeanClusterConfidence.Rd -------------------------------------------------------------------------------- /man/getProteinParameters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/getProteinParameters.Rd -------------------------------------------------------------------------------- /man/getRNAprofiles.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/getRNAprofiles.Rd -------------------------------------------------------------------------------- /man/getSpatialContext.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/getSpatialContext.Rd -------------------------------------------------------------------------------- /man/get_anchor_stats.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/get_anchor_stats.Rd -------------------------------------------------------------------------------- /man/get_neighborhood_expression.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/get_neighborhood_expression.Rd -------------------------------------------------------------------------------- /man/human_signature.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/human_signature.Rd -------------------------------------------------------------------------------- /man/insitutype.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/insitutype.Rd -------------------------------------------------------------------------------- /man/insitutypeML.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/insitutypeML.Rd -------------------------------------------------------------------------------- /man/iocolors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/iocolors.Rd -------------------------------------------------------------------------------- /man/ioprofiles.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/ioprofiles.Rd -------------------------------------------------------------------------------- /man/ismax.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/ismax.Rd -------------------------------------------------------------------------------- /man/lldist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/lldist.Rd -------------------------------------------------------------------------------- /man/lls_protein.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/lls_protein.Rd -------------------------------------------------------------------------------- /man/lls_rna.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/lls_rna.Rd -------------------------------------------------------------------------------- /man/logliks2probs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/logliks2probs.Rd -------------------------------------------------------------------------------- /man/mini_nsclc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/mini_nsclc.Rd -------------------------------------------------------------------------------- /man/mouse_signature.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/mouse_signature.Rd -------------------------------------------------------------------------------- /man/nbclust.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/nbclust.Rd -------------------------------------------------------------------------------- /man/nearestNeighborGraph.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/nearestNeighborGraph.Rd -------------------------------------------------------------------------------- /man/neighbor_colMeans.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/neighbor_colMeans.Rd -------------------------------------------------------------------------------- /man/neighbor_colSums.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/neighbor_colSums.Rd -------------------------------------------------------------------------------- /man/numCores.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/numCores.Rd -------------------------------------------------------------------------------- /man/prepDataForSketching.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/prepDataForSketching.Rd -------------------------------------------------------------------------------- /man/probs2logliks.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/probs2logliks.Rd -------------------------------------------------------------------------------- /man/radiusBasedGraph.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/radiusBasedGraph.Rd -------------------------------------------------------------------------------- /man/refineAnchors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/refineAnchors.Rd -------------------------------------------------------------------------------- /man/refineClusters.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/refineClusters.Rd -------------------------------------------------------------------------------- /man/spatialUpdate.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/spatialUpdate.Rd -------------------------------------------------------------------------------- /man/tonsil_annotation.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/tonsil_annotation.Rd -------------------------------------------------------------------------------- /man/tonsil_protein.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/tonsil_protein.Rd -------------------------------------------------------------------------------- /man/tonsil_reference_profile.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/tonsil_reference_profile.Rd -------------------------------------------------------------------------------- /man/updateProfilesFromAnchors.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/updateProfilesFromAnchors.Rd -------------------------------------------------------------------------------- /man/updateReferenceProfiles.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/updateReferenceProfiles.Rd -------------------------------------------------------------------------------- /man/update_logliks_with_cohort_freqs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/man/update_logliks_with_cohort_freqs.Rd -------------------------------------------------------------------------------- /reqs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/reqs.md -------------------------------------------------------------------------------- /specs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/specs.md -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/Makevars.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/src/Makevars.win -------------------------------------------------------------------------------- /src/RcppExports.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/src/RcppExports.cpp -------------------------------------------------------------------------------- /src/rcpparma_dnbinom_sparse.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/src/rcpparma_dnbinom_sparse.cpp -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-colorCellTypes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test-colorCellTypes.R -------------------------------------------------------------------------------- /tests/testthat/test_RCppExports.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_RCppExports.R -------------------------------------------------------------------------------- /tests/testthat/test_flightpath.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_flightpath.R -------------------------------------------------------------------------------- /tests/testthat/test_getProfiles.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_getProfiles.R -------------------------------------------------------------------------------- /tests/testthat/test_getSpatialContext.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_getSpatialContext.R -------------------------------------------------------------------------------- /tests/testthat/test_insitutype_Protein.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_insitutype_Protein.R -------------------------------------------------------------------------------- /tests/testthat/test_insitutype_RNA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_insitutype_RNA.R -------------------------------------------------------------------------------- /tests/testthat/test_refinecells_cell_merging_logic.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_refinecells_cell_merging_logic.R -------------------------------------------------------------------------------- /tests/testthat/test_spatialUpdate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/tests/testthat/test_spatialUpdate.R -------------------------------------------------------------------------------- /vignettes/NSCLC-RNA_InsituType-vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-RNA_InsituType-vignette.Rmd -------------------------------------------------------------------------------- /vignettes/NSCLC-RNA_InsituType-vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-RNA_InsituType-vignette.html -------------------------------------------------------------------------------- /vignettes/NSCLC-clustering-SingleCellExperiment-vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-clustering-SingleCellExperiment-vignette.Rmd -------------------------------------------------------------------------------- /vignettes/NSCLC-clustering-SingleCellExperiment-vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-clustering-SingleCellExperiment-vignette.html -------------------------------------------------------------------------------- /vignettes/NSCLC-clustering-vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-clustering-vignette.Rmd -------------------------------------------------------------------------------- /vignettes/NSCLC-clustering-vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-clustering-vignette.html -------------------------------------------------------------------------------- /vignettes/NSCLC-semi-supervised-cell-typing-vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-semi-supervised-cell-typing-vignette.Rmd -------------------------------------------------------------------------------- /vignettes/NSCLC-semi-supervised-cell-typing-vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-semi-supervised-cell-typing-vignette.html -------------------------------------------------------------------------------- /vignettes/NSCLC-supervised-cell-typing-vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-supervised-cell-typing-vignette.Rmd -------------------------------------------------------------------------------- /vignettes/NSCLC-supervised-cell-typing-vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/NSCLC-supervised-cell-typing-vignette.html -------------------------------------------------------------------------------- /vignettes/TONSIL_Protein_Insitu_Cell_Typing-vignette.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/TONSIL_Protein_Insitu_Cell_Typing-vignette.Rmd -------------------------------------------------------------------------------- /vignettes/TONSIL_Protein_Insitu_Cell_Typing-vignette.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Nanostring-Biostats/InSituType/HEAD/vignettes/TONSIL_Protein_Insitu_Cell_Typing-vignette.html --------------------------------------------------------------------------------