Files in stemangiola/sccomp
Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/rworkflows.yml
.gitignore
DESCRIPTION
NAMESPACE
R/data.R
R/functions_dirichlet_multinomial.R
R/functions_multi_beta.R
R/functions_multi_beta_binomial.R
R/methods.R
R/methods_OLD_framework.R
R/nanny.R
R/sccomp-package.R
R/stanmodels.R
R/utilities.R
R/validation.R
README.Rmd
README.md
configure
configure.win
data/counts_obj.rda
data/glm_dirichlet_multinomial.rda
data/glm_dirichlet_multinomial_generate_quantities.rda
data/glm_dirichlet_multinomial_imputation.rda
data/glm_multi_beta.rda
data/glm_multi_beta_generate_data.rda
data/multipanel_theme.rda
data/sce_obj.rda
data/seurat_obj.rda
dev/.gitignore
dev/attach.R
dev/bench_pipeline/calculate_auc.R
dev/bench_pipeline/create_input.R
dev/bench_pipeline/create_makefile.R
dev/bench_pipeline/estimate_dirichletMultinomial.R
dev/bench_pipeline/estimate_rest.R
dev/bench_pipeline/estimate_sccomp.R
dev/bench_pipeline/parse_estimates.R
dev/bench_pipeline/plot_results.R
dev/bench_pipeline_hyperprior/calculate_auc.R
dev/bench_pipeline_hyperprior/create_input.R
dev/bench_pipeline_hyperprior/create_makefile.R
dev/bench_pipeline_hyperprior/estimate_sccomp.R
dev/bench_pipeline_hyperprior/parse_estimates.R
dev/bench_pipeline_hyperprior/plot_results.R
dev/data_integration/calculate_UMAP.R
dev/data_integration/estimate_datasets_and_save.R
dev/data_integration/estimate_datasets_and_save_dirichlet_multinomial.R
dev/stan_models/glm_beta_binomial.stan
dev/stan_models/glm_dirichlet_multinomial.stan
dev/stan_models/glm_dirichlet_multinomial_generate_quantities.stan
dev/stan_models/glm_dirichlet_multinomial_imputation.stan
dev/stan_models/glm_multi_beta.stan
dev/stan_models/glm_multi_beta_generate_data.stan
dev/stan_models/glm_multinomial_logit_linear_simulate_data.stan
dev/test_influence_of_priors.R
dev/zzz.R
inst/.gitignore
inst/CITATION
inst/NEWS.rd
inst/figures/unnamed-chunk-10-1.png
inst/figures/unnamed-chunk-11-1.png
inst/figures/unnamed-chunk-12-1.png
inst/figures/unnamed-chunk-13-1.png
inst/figures/unnamed-chunk-14-1.png
inst/figures/unnamed-chunk-15-1.png
inst/figures/unnamed-chunk-16-1.png
inst/figures/unnamed-chunk-17-1.png
inst/figures/unnamed-chunk-18-1.png
inst/figures/unnamed-chunk-19-1.png
inst/figures/unnamed-chunk-4-1.png
inst/figures/unnamed-chunk-5-1.png
inst/figures/unnamed-chunk-6-1.png
inst/figures/unnamed-chunk-7-1.png
inst/figures/unnamed-chunk-8-1.png
inst/figures/unnamed-chunk-9-1.png
inst/figures/unnamed-chunk-9-2.png
inst/include/stan_meta_header.hpp
inst/logo-01.png
inst/stan/.gitignore
inst/stan/glm_multi_beta_binomial.stan
inst/stan/glm_multi_beta_binomial_generate_date.stan
inst/stan/glm_multi_beta_binomial_simulate_data.stan
inst/stan/include/license.stan
man/counts_obj.Rd
man/fragments/intro.Rmd
man/glm_dirichlet_multinomial.Rd
man/glm_dirichlet_multinomial_generate_quantities.Rd
man/glm_dirichlet_multinomial_imputation.Rd
man/glm_multi_beta.Rd
man/glm_multi_beta_generate_data.Rd
man/multi_beta_glm.Rd
man/multipanel_theme.Rd
man/plot.sccomp_tbl.Rd
man/plot_summary.Rd
man/sccomp-package.Rd
man/sccomp_boxplot.Rd
man/sccomp_estimate.Rd
man/sccomp_glm.Rd
man/sccomp_predict.Rd
man/sccomp_remove_outliers.Rd
man/sccomp_remove_unwanted_variation.Rd
man/sccomp_replicate.Rd
man/sccomp_test.Rd
man/sce_obj.Rd
man/seurat_obj.Rd
man/simulate_data.Rd
man/test_contrasts.Rd
src/.gitignore
src/Makevars
src/Makevars.win
tests/testthat.R
tests/testthat/test-old_framework.R
tests/testthat/test-sccomp_.R
vignettes/figures/logo-01.png
vignettes/introduction.Rmd
