├── .Rbuildignore ├── .circleci └── config.yml ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── argument_checking.R ├── fastglmpca-package.R ├── fit.R ├── init.R ├── loglik.R ├── methods.R ├── pbmc_facs.R ├── simulate_data.R ├── threads.R └── utils.R ├── README.md ├── _pkgdown.yml ├── appveyor.yml ├── cran-comments.md ├── data └── pbmc_facs.RData ├── docs ├── 404.html ├── LICENSE-text.html ├── articles │ ├── index.html │ ├── intro_fastglmpca.html │ └── intro_fastglmpca_files │ │ └── figure-html │ │ ├── fitted-vs-observed-1.png │ │ └── plot-v-1.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── fit_glmpca_pois.html │ ├── fitted.glmpca_pois_fit.html │ ├── generate_glmpca_data_pois.html │ ├── index.html │ ├── pbmc_facs.html │ ├── set_fastglmpca_threads.html │ └── summary.glmpca_pois_fit.html └── sitemap.xml ├── inst ├── analysis │ ├── PC1_2_seurat.R │ ├── check_loglik_calcs.R │ ├── compute_droplet_cellwise_logliks.R │ ├── compute_pbmc_cellwise_logliks.R │ ├── droplets_PC1_10.R │ ├── examine_droplet_logliks.R │ ├── loglik_plots.R │ ├── main_fig.R │ ├── make_Rdata.R │ ├── pbmc_PC1_10.R │ ├── pca_pbmc_better.R │ ├── plot_runtime_scaling.R │ ├── results.RData │ ├── time_until_better.R │ └── tsne_droplet.R ├── code │ ├── droplet_demo.R │ ├── fastglmpca_vs_glmpca.R │ ├── fit_rank1.R │ ├── fit_rank2.R │ ├── glmpca_vs_sinkhorn.R │ ├── loglik.R │ ├── monitor_memory.py │ ├── pbmc_facs_demo.R │ ├── poisglm_approx.R │ ├── poly_exp.R │ ├── sparse_benchmark.R │ └── test_fastglmpca.R ├── datasets │ └── newsgroups.RData ├── experiments │ ├── fit_droplets_daarem_fastglmpca_28core.R │ ├── fit_droplets_fastglmpca_1core.R │ ├── fit_droplets_fastglmpca_28core.R │ ├── fit_droplets_glmpca.R │ ├── fit_droplets_scGBM.R │ ├── fit_pbmc_daarem_fastglmpca_28core.R │ ├── fit_pbmc_fastglmpca_1core.R │ ├── fit_pbmc_fastglmpca_28core.R │ ├── fit_pbmc_glmpca.R │ ├── fit_pbmc_scGBM.R │ ├── run_seurat_droplets.R │ ├── run_seurat_pbmc.R │ └── runtime_scaling.R └── scratch │ ├── ccd_testing.R │ ├── default_test.R │ ├── fit_droplets_glmpca.R │ ├── fit_droplets_plash.R │ ├── fit_pbmc_glmpca.R │ ├── fit_pbmc_plash.R │ ├── glmpca_data_sim_res.csv │ ├── glmpca_sim.R │ ├── negative_binomial_deriv.R │ ├── nloptr_scratch.R │ ├── nmf_data_sim_res.csv │ ├── nmf_sim.R │ ├── pbmc_facs_fit.R │ ├── plash_testing.R │ ├── saved_models │ └── plash_pbmc_nloptr_fit.rds │ ├── sim_model_comparison.Rmd │ ├── sim_res.Rmd │ ├── sim_res.html │ ├── sim_res2.Rmd │ ├── sim_res2.html │ ├── test_projection_method.R │ └── variable_c_sim.R ├── man ├── fit_glmpca_pois.Rd ├── fitted.glmpca_pois_fit.Rd ├── generate_glmpca_data_pois.Rd ├── pbmc_facs.Rd ├── set_fastglmpca_threads.Rd └── summary.glmpca_pois_fit.Rd ├── src ├── 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