Files in lulizou/spASE
Detecting Allele-Specific Expression in Spatial Transcriptomics
.DS_Store
.Rbuildignore
.gitignore
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/betabinase.R
R/classes.R
R/cside_spase.R
R/expit.R
R/getSplineMatrix.R
R/platform_effect_normalization.R
R/plotScase.R
R/plotSpase.R
R/plotting.R
R/postProcessing.R
R/prob_model.R
R/processRef.R
R/quasibinase.R
R/replintegrate.R
R/repliterate.R
R/runRCTD.R
R/scase.R
R/spASE_utils.R
R/spacexr.R
R/spase.R
R/spase_sim_utils.R
R/test.R
R/test2.R
R/utils.R
README.md
README.qmd
analysis/.DS_Store
analysis/00_preprocess.md
analysis/00_preprocess.qmd
analysis/01_cell_type_maps.md
analysis/01_cell_type_maps.qmd
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-11-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-12-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-14-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-15-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-3-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-5-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-7-1.png
analysis/01_cell_type_maps_files/figure-commonmark/unnamed-chunk-9-1.png
analysis/02_compare_visium_slideseq_cerebellum.md
analysis/02_compare_visium_slideseq_cerebellum.qmd
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-10-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-11-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-13-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-14-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-15-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-3-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-5-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-6-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-7-1.png
analysis/02_compare_visium_slideseq_cerebellum_files/figure-commonmark/unnamed-chunk-9-1.png
analysis/03_simulation_cere3.R
analysis/03_simulation_cere4.R
analysis/03_simulations.md
analysis/03_simulations.qmd
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-12-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-13-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-14-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-15-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-3-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-4-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-5-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-7-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-8-1.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-8-2.png
analysis/03_simulations_files/figure-commonmark/unnamed-chunk-8-3.png
analysis/03_simulations_files/figure-html/unnamed-chunk-12-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-13-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-14-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-15-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-3-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-4-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-5-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-7-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-8-1.png
analysis/03_simulations_files/figure-html/unnamed-chunk-8-2.png
analysis/03_simulations_files/figure-html/unnamed-chunk-8-3.png
analysis/03_simulations_files/libs/bootstrap/bootstrap-icons.css
analysis/03_simulations_files/libs/bootstrap/bootstrap-icons.woff
analysis/03_simulations_files/libs/bootstrap/bootstrap.min 2.css
analysis/03_simulations_files/libs/bootstrap/bootstrap.min.css
analysis/03_simulations_files/libs/bootstrap/bootstrap.min.js
analysis/03_simulations_files/libs/clipboard/clipboard.min.js
analysis/03_simulations_files/libs/quarto-html/anchor.min.js
analysis/03_simulations_files/libs/quarto-html/popper.min.js
analysis/03_simulations_files/libs/quarto-html/quarto-syntax-highlighting.css
analysis/03_simulations_files/libs/quarto-html/quarto.js
analysis/03_simulations_files/libs/quarto-html/tippy.css
analysis/03_simulations_files/libs/quarto-html/tippy.umd.min.js
analysis/04_overall_results_summary_figures.md
analysis/04_overall_results_summary_figures.qmd
analysis/05_celltype_xchr_figures.md
analysis/05_celltype_xchr_figures.qmd
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-11-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-11-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-11-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-11-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-11-5.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-12-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-12-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-12-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-13-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-13-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-13-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-10.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-5.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-6.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-7.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-8.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-17-9.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-20-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-20-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-20-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-10.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-5.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-6.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-7.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-8.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-23-9.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-25-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-25-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-25-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-25-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-25-5.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-25-6.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-28-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-28-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-28-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-29-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-29-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-29-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-29-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-32-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-32-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-32-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-33-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-33-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-33-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-33-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-36-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-4-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-4-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-6-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-6-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-8-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-8-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-8-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-8-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-9-1.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-9-2.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-9-3.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-9-4.png
analysis/05_celltype_xchr_figures_files/figure-commonmark/unnamed-chunk-9-5.png
analysis/06_visium_slideseq_mixtures_overdispersion.md
analysis/06_visium_slideseq_mixtures_overdispersion.qmd
analysis/06_visium_slideseq_mixtures_overdispersion_files/figure-commonmark/unnamed-chunk-11-1.png
analysis/06_visium_slideseq_mixtures_overdispersion_files/figure-commonmark/unnamed-chunk-12-1.png
analysis/06_visium_slideseq_mixtures_overdispersion_files/figure-html/unnamed-chunk-11-1.png
analysis/06_visium_slideseq_mixtures_overdispersion_files/figure-html/unnamed-chunk-12-1.png
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/bootstrap/bootstrap-icons.css
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/bootstrap/bootstrap-icons.woff
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/bootstrap/bootstrap.min.css
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/bootstrap/bootstrap.min.js
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/clipboard/clipboard.min.js
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/quarto-html/anchor.min.js
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/quarto-html/popper.min.js
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/quarto-html/quarto-syntax-highlighting.css
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/quarto-html/quarto.js
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/quarto-html/tippy.css
analysis/06_visium_slideseq_mixtures_overdispersion_files/libs/quarto-html/tippy.umd.min.js
analysis/07_129_CAST_analysis.md
analysis/07_129_CAST_analysis.qmd
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-10-1.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-11-1.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-14-1.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-6-1.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-6-2.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-6-3.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-6-4.png
analysis/07_129_CAST_analysis_files/figure-commonmark/unnamed-chunk-6-5.png
analysis/08_xchr_inactivation.md
analysis/08_xchr_inactivation.qmd
analysis/08_xchr_inactivation_files/libs/bootstrap/bootstrap-icons.css
analysis/08_xchr_inactivation_files/libs/bootstrap/bootstrap-icons.woff
analysis/08_xchr_inactivation_files/libs/bootstrap/bootstrap.min.css
analysis/08_xchr_inactivation_files/libs/bootstrap/bootstrap.min.js
analysis/08_xchr_inactivation_files/libs/clipboard/clipboard.min.js
analysis/08_xchr_inactivation_files/libs/quarto-html/anchor.min.js
analysis/08_xchr_inactivation_files/libs/quarto-html/popper.min.js
analysis/08_xchr_inactivation_files/libs/quarto-html/quarto-syntax-highlighting.css
analysis/08_xchr_inactivation_files/libs/quarto-html/quarto.js
analysis/08_xchr_inactivation_files/libs/quarto-html/tippy.css
analysis/08_xchr_inactivation_files/libs/quarto-html/tippy.umd.min.js
analysis/09_distributions.qmd
analysis/README.md
analysis/cere_3_slideseq_barcodes.tsv
analysis/cere_3_slideseq_genes.tsv
analysis/cere_4_visium_barcodes.tsv
analysis/cere_4_visium_genes.tsv
analysis/hippo_1_slideseq_barcodes.tsv
analysis/hippo_1_slideseq_genes.tsv
analysis/hippo_2_slideseq_barcodes.tsv
analysis/hippo_2_slideseq_genes.tsv
analysis/hippo_3_slideseq_barcodes.tsv
analysis/hippo_3_slideseq_genes.tsv
analysis/logs/de_log.txt
analysis/logs/spase_log.txt
analysis/run_rctd.sbatch
analysis/run_simulations_cere3.sbatch
analysis/run_simulations_cere4.sbatch
analysis/run_spase.sbatch
analysis/run_spase_celltype.sbatch
analysis/run_spase_overall_bias.sbatch
analysis/run_spase_overall_spatial.sbatch
analysis/scripts/create_mtx.R
analysis/scripts/run_rctd_cere3.R
analysis/scripts/run_rctd_cere4_visium.R
analysis/scripts/run_rctd_hippo1.R
analysis/scripts/run_rctd_hippo2.R
analysis/scripts/run_rctd_hippo3.R
analysis/scripts/run_rctd_mix5_visium.R
analysis/scripts/run_spase_cere3_celltype.R
analysis/scripts/run_spase_cere3_overall_bias.R
analysis/scripts/run_spase_cere3_overall_spatial.R
analysis/scripts/run_spase_cere4_visium_celltype.R
analysis/scripts/run_spase_cere4_visium_overall_bias.R
analysis/scripts/run_spase_cere4_visium_overall_spatial.R
analysis/scripts/run_spase_hippo1_celltype.R
analysis/scripts/run_spase_hippo1_overall_bias.R
analysis/scripts/run_spase_hippo1_overall_spatial.R
analysis/scripts/run_spase_hippo2_celltype.R
analysis/scripts/run_spase_hippo2_overall_bias.R
analysis/scripts/run_spase_hippo2_overall_spatial.R
analysis/scripts/run_spase_hippo3_celltype.R
analysis/scripts/run_spase_hippo3_overall_bias.R
analysis/scripts/run_spase_hippo3_overall_spatial.R
analysis/scripts/run_spase_mix5_visium_overall_bias.R
analysis/scripts/run_spase_mix5_visium_overall_spatial.R
analysis/simulation_results_cere3.csv
analysis/simulation_results_cere4.csv
analysis/simulations_cere3_params.tsv
analysis/simulations_cere4_params.tsv
analysis/tables/03_supp_table_celltype_bias.csv
analysis/tables/03_supp_table_overall_bias.csv
analysis/tables/03_supp_table_spatial_celltype_bias.csv
analysis/tables/03_supp_table_spatial_overall_bias.csv
analysis/tables/04_supp_table_celltype_bias.csv
analysis/tables/04_supp_table_overall_bias.csv
analysis/tables/04_supp_table_spatial_celltype_bias.csv
analysis/tables/04_supp_table_spatial_overall_bias.csv
inst/extdata/MGImarkerQuery_20190611_114216.txt
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/jaspar-mouse-1.csv
inst/extdata/jaspar-mouse-2.csv
inst/extdata/jaspar-mouse-3.csv
inst/extdata/reference_scrna/cerebellum_sn_ref_spacexr.rds
inst/extdata/reference_scrna/ref_coarse_10000.rds
inst/extdata/reference_scrna/scRefSubsampled1000.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/betabinase.Rd
man/build.designmatrix.intercept.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/cside_spase.Rd
man/expit.Rd
man/exvar.celltocell.interactions.Rd
man/exvar.point.density.Rd
man/fitBulk.Rd
man/fitPixels.Rd
man/getSplineMatrix.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/plotScase.Rd
man/plotSpase.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/quasibinase.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.intercept.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/scase.Rd
man/set_cell_types_assigned.Rd
man/set_likelihood_vars.Rd
man/spacexr.Rd
man/spase.Rd
man/write_de_summary.Rd
scripts/processBowtie2.py
spASE.Rproj
vignettes/.DS_Store
vignettes/README.md
vignettes/demo.Rmd
vignettes/figures2-4-slideseq 2.html
vignettes/figures2-4-slideseq.Rmd
vignettes/suppfigure-CI-plots.Rmd
vignettes/suppfigure-CI-sim.Rmd
vignettes/suppfigure-ptgds-scatac-rnaseq.Rmd
vignettes/suppfigure-simulation1-plots.Rmd
vignettes/suppfigure-simulation1.Rmd
