dmcable/RCTD
SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

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dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics
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SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

AnalysisCSIDE/Figures/figure2.Rmd
AnalysisCSIDE/Figures/figure2.html
AnalysisCSIDE/Figures/figure3.Rmd
AnalysisCSIDE/Figures/figure3.html
AnalysisCSIDE/Figures/figure4_j20.Rmd
AnalysisCSIDE/Figures/figure4_j20.html
AnalysisCSIDE/Figures/figure4_merfish.Rmd
AnalysisCSIDE/Figures/figure4_merfish.html
AnalysisCSIDE/Figures/figure4_testes.Rmd
AnalysisCSIDE/Figures/figure4_testes.html
AnalysisCSIDE/Figures/figure4_visium.Rmd
AnalysisCSIDE/Figures/figure4_visium.html
AnalysisCSIDE/Figures/figure5_nonparametric.Rmd
AnalysisCSIDE/Figures/figure5_nonparametric.html
AnalysisCSIDE/Figures/figure5_parametric.Rmd
AnalysisCSIDE/Figures/figure5_parametric.html
AnalysisCSIDE/Figures/supp1.Rmd AnalysisCSIDE/Figures/supp2.Rmd AnalysisCSIDE/Figures/supp3.Rmd AnalysisCSIDE/Figures/supp4.Rmd AnalysisCSIDE/Figures/supp5.Rmd AnalysisCSIDE/Figures/supp6.Rmd AnalysisCSIDE/Figures/supp7.Rmd AnalysisCSIDE/Figures/supp8.Rmd AnalysisCSIDE/Preprocessing_and_RCTD/cer_reps.R AnalysisCSIDE/Preprocessing_and_RCTD/run_RCTD_testes.R AnalysisCSIDE/README.Rmd AnalysisCSIDE/README.md AnalysisCSIDE/helper_functions/alzheimers_helper.R AnalysisCSIDE/helper_functions/de_simulation_helper.R AnalysisCSIDE/helper_functions/merge_de_helper.R AnalysisCSIDE/helper_functions/personal_utils.R AnalysisCSIDE/helper_functions/testes_helper.R AnalysisCSIDE/image_analysis/hcr.R AnalysisCSIDE/image_analysis/overlay.R AnalysisCSIDE/j20/align_plaque_density.R AnalysisCSIDE/j20/create_pd.R AnalysisCSIDE/j20/pd_to_exvar.R AnalysisCSIDE/j20/preprocess_j20.R AnalysisCSIDE/j20/run_CSIDE_j20_21.R AnalysisCSIDE/j20/run_CSIDE_j20_22.R AnalysisCSIDE/j20/run_CSIDE_j20_23.R AnalysisCSIDE/j20/run_CSIDE_j20_24.R AnalysisCSIDE/j20/run_RCTD_j20_21.R AnalysisCSIDE/j20/run_RCTD_j20_22.R AnalysisCSIDE/j20/run_RCTD_j20_23.R AnalysisCSIDE/j20/run_RCTD_j20_24.R
AnalysisCSIDE/paper_results/MERFISH_linear_de/Astrocytes.csv
AnalysisCSIDE/paper_results/MERFISH_linear_de/Endothelial.csv
AnalysisCSIDE/paper_results/MERFISH_linear_de/Excitatory.csv
AnalysisCSIDE/paper_results/MERFISH_linear_de/Immature oligodendrocyte.csv
AnalysisCSIDE/paper_results/MERFISH_linear_de/Inhibitory.csv
AnalysisCSIDE/paper_results/MERFISH_linear_de/Mature oligodendrocyte.csv
AnalysisCSIDE/paper_results/MERFISH_quadratic_de/Astrocytes.csv
AnalysisCSIDE/paper_results/MERFISH_quadratic_de/Endothelial.csv
AnalysisCSIDE/paper_results/MERFISH_quadratic_de/Excitatory.csv
AnalysisCSIDE/paper_results/MERFISH_quadratic_de/Immature oligodendrocyte.csv
AnalysisCSIDE/paper_results/MERFISH_quadratic_de/Inhibitory.csv
AnalysisCSIDE/paper_results/MERFISH_quadratic_de/Mature oligodendrocyte.csv
AnalysisCSIDE/paper_results/cerebellum_population/Astrocytes_cell_type_genes.csv
AnalysisCSIDE/paper_results/cerebellum_population/Bergmann_cell_type_genes.csv
AnalysisCSIDE/paper_results/cerebellum_population/Granule_cell_type_genes.csv
AnalysisCSIDE/paper_results/cerebellum_population/Oligodendrocytes_cell_type_genes.csv
AnalysisCSIDE/paper_results/cerebellum_population/Purkinje_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/Astrocyte_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/CA1_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/CA3_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/Denate_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/Interneuron_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/Microglia_Macrophages_cell_type_genes.csv
AnalysisCSIDE/paper_results/j20_population/Oligodendrocyte_cell_type_genes.csv
AnalysisCSIDE/paper_results/testes/ES.csv
AnalysisCSIDE/paper_results/testes/RS.csv
AnalysisCSIDE/paper_results/testes/SPC.csv
AnalysisCSIDE/paper_results/testes/SPG.csv
AnalysisCSIDE/paper_results/testes/Sertoli.csv
AnalysisCSIDE/paper_results/tumor_nonparametric/CAF.csv
AnalysisCSIDE/paper_results/tumor_nonparametric/monocyte_DC.csv
AnalysisCSIDE/paper_results/tumor_nonparametric/vascular smooth mc.csv
AnalysisCSIDE/paper_results/tumor_parametric/CAF.csv
AnalysisCSIDE/paper_results/tumor_parametric/hepatocyte 2.csv
AnalysisCSIDE/paper_results/tumor_parametric/vascular smooth mc.csv
AnalysisCSIDE/run_CSIDE/run_de_cer_08.R AnalysisCSIDE/run_CSIDE/run_de_cer_09.R AnalysisCSIDE/run_CSIDE/run_de_cer_11.R AnalysisCSIDE/run_CSIDE/run_de_merfish.R AnalysisCSIDE/run_CSIDE/run_de_nonparametric.R AnalysisCSIDE/run_CSIDE/run_de_testes.R AnalysisCSIDE/run_CSIDE/run_de_tumor.R AnalysisPaper/MainFigures/Updated-Compatability/figure2-platform-effect.Rmd AnalysisPaper/MainFigures/figure1.Rmd
AnalysisPaper/MainFigures/figure1.html
AnalysisPaper/MainFigures/figure2-platform-effect.Rmd
AnalysisPaper/MainFigures/figure2-platform-effect.html
AnalysisPaper/MainFigures/figure2.Rmd
AnalysisPaper/MainFigures/figure2.html
AnalysisPaper/MainFigures/figure3.Rmd
AnalysisPaper/MainFigures/figure3.html
AnalysisPaper/MainFigures/figure4.Rmd
AnalysisPaper/MainFigures/figure4.html
AnalysisPaper/MainFigures/figure5-all.Rmd
AnalysisPaper/MainFigures/figure5-all.html
AnalysisPaper/MainFigures/figure5-interneurons.Rmd
AnalysisPaper/MainFigures/figure5-interneurons.html
AnalysisPaper/MainFigures/figure6-astrocytes.Rmd
AnalysisPaper/MainFigures/figure6-astrocytes.html
AnalysisPaper/MainFigures/figure6-spatialgenes.Rmd
AnalysisPaper/MainFigures/figure6-spatialgenes.html
AnalysisPaper/Plotting/figure_utils.R AnalysisPaper/README.Rmd AnalysisPaper/README.md AnalysisPaper/Rscripts/doubletsimulation.R AnalysisPaper/Rscripts/dropSeqProcess.R AnalysisPaper/Rscripts/prepareNMF.R AnalysisPaper/Rscripts/processNMF.R AnalysisPaper/Rscripts/processVisium.R AnalysisPaper/Rscripts/subcluster.R AnalysisPaper/Rscripts/weightDecompose.R AnalysisPaper/SuppFigures/supp.Rmd AnalysisPaper/SuppFigures/supp_part2.Rmd
AnalysisPaper/conf/dataset.yml
AnalysisPaper/conf/datasetCerPuck.yml
AnalysisPaper/conf/datasetCross.yml
AnalysisPaper/conf/datasetHippoInterneuron.yml
AnalysisPaper/conf/datasetHippoPuck.yml
AnalysisPaper/conf/datasetInterneuronCoarse.yml
AnalysisPaper/conf/default.yml
AnalysisPaper/conf/hippo.yml
AnalysisPaper/conf/interneuron.yml
AnalysisPaper/conf/interneuron_coarse.yml
DESCRIPTION
LICENSE
NAMESPACE
R/CSIDE.R R/CSIDE_class.R R/CSIDE_helper.R R/CSIDE_plots.R R/CSIDE_population.R R/CSIDE_stats.R R/CSIDE_utils.R R/IRWLS.R R/RCTD_helper.R R/RCTDreplicates.R R/Reference.R R/SpatialRNA.R R/classes.R R/platform_effect_normalization.R R/plotting.R R/postProcessing.R R/prob_model.R R/processRef.R R/replintegrate.R R/repliterate.R R/runRCTD.R R/spacexr.R R/utils.R README.Rmd README.md documentation/README.Rmd documentation/README.md
inst/extdata/.DS_Store
inst/extdata/Qmat/Q_mat_1.rds
inst/extdata/Qmat/Q_mat_2.rds
inst/extdata/Qmat/Q_mat_3.rds
inst/extdata/Qmat/Q_mat_4.rds
inst/extdata/Qmat/Q_mat_5.rds
inst/extdata/Qmat/X_vals.rds
inst/extdata/Reference/.DS_Store
inst/extdata/Reference/Merfish_Ref/cell_types.csv
inst/extdata/Reference/Merfish_Ref/counts.csv
inst/extdata/Reference/Merfish_Ref/nUMI.csv
inst/extdata/Reference/Vignette/.DS_Store
inst/extdata/Reference/Vignette/cell_type_dict.csv
inst/extdata/Reference/Vignette/dge.csv
inst/extdata/Reference/Vignette/meta_data.csv
inst/extdata/Reference/Visium_Lymph_Ref/ref_downsampled.rds
inst/extdata/Reference/Visium_Ref/cell_types.csv
inst/extdata/Reference/Visium_Ref/counts.csv
inst/extdata/Reference/Visium_Ref/nUMI.csv
inst/extdata/SpatialRNA/.DS_Store
inst/extdata/SpatialRNA/MerfishVignette/coords.csv
inst/extdata/SpatialRNA/MerfishVignette/counts.csv
inst/extdata/SpatialRNA/MerfishVignette/nUMI.csv
inst/extdata/SpatialRNA/Vignette/.DS_Store
inst/extdata/SpatialRNA/Vignette/BeadLocationsForR.csv
inst/extdata/SpatialRNA/Vignette/MappedDGEForR.csv
inst/extdata/SpatialRNA/Vignette_rep2/BeadLocationsForR.csv
inst/extdata/SpatialRNA/Vignette_rep2/MappedDGEForR.csv
inst/extdata/SpatialRNA/Vignette_rep3/BeadLocationsForR.csv
inst/extdata/SpatialRNA/Vignette_rep3/MappedDGEForR.csv
inst/extdata/SpatialRNA/Vignette_rep4/BeadLocationsForR.csv
inst/extdata/SpatialRNA/Vignette_rep4/MappedDGEForR.csv
inst/extdata/SpatialRNA/VisiumLymphVignette/coords.rds
inst/extdata/SpatialRNA/VisiumLymphVignette/expr.rds
inst/extdata/SpatialRNA/VisiumVignette/coords.csv
inst/extdata/SpatialRNA/VisiumVignette/counts.csv
inst/extdata/SpatialRNA/VisiumVignette/nUMI.csv
inst/extdata/SpatialRNA/VisiumVignette/testes_sig_gene_list.rds
man/CSIDE.population.inference.Rd man/RCTD-class.Rd man/RCTD.replicates-class.Rd man/Reference-class.Rd man/Reference.Rd man/SpatialRNA-class.Rd man/SpatialRNA.Rd man/aggregate_cell_types.Rd man/build.designmatrix.nonparam.Rd man/build.designmatrix.regions.Rd man/build.designmatrix.single.Rd man/choose_sigma_c.Rd man/convert.old.RCTD.Rd man/count_cell_types.Rd man/create.RCTD.Rd man/create.RCTD.replicates.Rd man/create_RCTD_plots.Rd man/exvar.celltocell.interactions.Rd man/exvar.point.density.Rd man/fitBulk.Rd man/fitPixels.Rd man/get_cell_type_info.Rd man/get_de_genes.Rd man/get_decomposed_data.Rd man/get_doublet_weights.Rd man/get_norm_ref.Rd man/get_standard_errors.Rd man/import_weights.Rd man/make_all_de_plots.Rd man/make_de_plots_genes.Rd man/make_de_plots_quant.Rd man/make_de_plots_regions.Rd man/make_de_plots_replicates.Rd man/make_de_plots_spatial.Rd man/merge_RCTD_objects.Rd man/normalize_weights.Rd man/plot_all_cell_types.Rd man/plot_class.Rd man/plot_cond_occur.Rd man/plot_doub_occur_stack.Rd man/plot_doublets.Rd man/plot_doublets_type.Rd man/plot_gene_raw.Rd man/plot_gene_regions.Rd man/plot_gene_two_regions.Rd man/plot_occur_unthreshold.Rd man/plot_prediction_gene.Rd man/plot_puck_continuous.Rd man/plot_puck_wrapper.Rd man/plot_weights.Rd man/plot_weights_doublet.Rd man/plot_weights_unthreshold.Rd man/process_beads_batch.Rd man/process_data.Rd man/read.SpatialRNA.Rd man/read.VisiumSpatialRNA.Rd man/restrict_counts.Rd man/restrict_puck.Rd man/run.CSIDE.Rd man/run.CSIDE.general.Rd man/run.CSIDE.nonparam.Rd man/run.CSIDE.regions.Rd man/run.CSIDE.replicates.Rd man/run.CSIDE.single.Rd man/run.RCTD.Rd man/run.RCTD.replicates.Rd man/save.CSIDE.replicates.Rd man/set_cell_types_assigned.Rd man/set_likelihood_vars.Rd man/spacexr.Rd man/write_de_summary.Rd
resources/RCTD_0.1.0.tar.gz
spacexr.Rproj
spacexr_manual_2.2.1.pdf vignettes/CSIDE_celltocell_interactions.Rmd
vignettes/CSIDE_celltocell_interactions.html
vignettes/CSIDE_pathology_interactions.Rmd
vignettes/CSIDE_pathology_interactions.html
vignettes/CSIDE_two_regions.Rmd
vignettes/CSIDE_two_regions.html
vignettes/README.Rmd vignettes/README.md vignettes/differential-expression.Rmd
vignettes/differential-expression.html
vignettes/merfish_nonparametric.Rmd
vignettes/merfish_nonparametric.html
vignettes/replicates.Rmd
vignettes/replicates.html
vignettes/spatial-transcriptomics.Rmd
vignettes/spatial-transcriptomics.html
vignettes/visium_CSIDE_celltocell_interactions.Rmd
vignettes/visium_CSIDE_celltocell_interactions.html
vignettes/visium_full_regions.Rmd
vignettes/visium_full_regions.html
vignettes/visium_multi.Rmd
vignettes/visium_multi.html
dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.

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