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
LICENSE
LICENSE.md
NAMESPACE
R/cmdstanr_safe.R
R/data.R
R/functions_multi_beta_binomial.R
R/methods.R
R/methods_OLD_framework.R
R/nanny.R
R/utilities.R
R/validation.R
README.Rmd
README.md
cleanup
cleanup.win
data/counts_obj.rda
data/multipanel_theme.rda
data/no_significance_df.rda
data/sce_obj.rda
data/seurat_obj.rda
dev/.gitignore
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/update_models_for_cmdstanr.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-20-1.png
inst/figures/unnamed-chunk-21-1.png
inst/figures/unnamed-chunk-22-1.png
inst/figures/unnamed-chunk-24-1.png
inst/figures/unnamed-chunk-25-1.png
inst/figures/unnamed-chunk-26-1.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/logo-01.png
inst/stan/.gitignore
inst/stan/glm_multi_beta_binomial.stan
inst/stan/glm_multi_beta_binomial_generate_data.stan
inst/stan/glm_multi_beta_binomial_simulate_data.stan
man/counts_obj.Rd
man/fragments/intro.Rmd
man/get_output_samples.Rd
man/multipanel_theme.Rd
man/no_significance_df.Rd
man/plot.sccomp_tbl.Rd
man/plot_1D_intervals.Rd
man/plot_2D_intervals.Rd
man/plot_scatterplot.Rd
man/sccomp_boxplot.Rd
man/sccomp_calculate_residuals.Rd
man/sccomp_estimate.Rd
man/sccomp_predict.Rd
man/sccomp_proportional_fold_change.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
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/helper-utils.R
tests/testthat/test-sccomp_.R
vignettes/introduction.Rmd
