Files in willwerscheid/flashier
Empirical Bayes Matrix Factorization
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/arg_checks.R
R/backfit.R
R/backfit_parallel.R
R/data.R
R/data_generics.R
R/data_lowrank.R
R/data_lrps.R
R/extrapolate.R
R/factor_add.R
R/factor_init.R
R/factor_update.R
R/flash.R
R/flash_add_intercept.R
R/flash_backfit.R
R/flash_conv_crit_fns.R
R/flash_ebnm.R
R/flash_factors_fix.R
R/flash_factors_init.R
R/flash_factors_remove.R
R/flash_factors_reorder.R
R/flash_fit_object.R
R/flash_greedy.R
R/flash_greedy_init_fns.R
R/flash_init.R
R/flash_methods.R
R/flash_nullcheck.R
R/flash_plots.R
R/flash_set_conv_crit.R
R/flash_set_timeout.R
R/flash_set_verbose.R
R/flash_update_data.R
R/flash_verbose_fns.R
R/helpers.R
R/objective.R
R/ops_fullrank.R
R/ops_lowrank.R
R/ops_r1.R
R/residuals_and_R2.R
R/sampler.R
R/set_data.R
R/tau.R
R/verbose_announcements.R
R/warmstart_sanity_check.R
R/wrapup.R
README.md
_pkgdown.yml
data-raw/gtex.R
data/gtex.rda
data/gtex_colors.rda
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/advanced_flashier.html
docs/articles/advanced_flashier_files/figure-html/fixed.sprs-1.png
docs/articles/advanced_flashier_files/figure-html/intercept-1.png
docs/articles/flashier_closer_look.html
docs/articles/flashier_closer_look_files/figure-html/backfit.plot-1.png
docs/articles/flashier_closer_look_files/figure-html/bf.compare-1.png
docs/articles/flashier_closer_look_files/figure-html/final.bf.ci.plot-1.png
docs/articles/flashier_closer_look_files/figure-html/gtex.bycol.plot-1.png
docs/articles/flashier_closer_look_files/figure-html/plot.bar-1.png
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docs/articles/flashier_closer_look_files/figure-html/unnamed-chunk-1-1.png
docs/articles/flashier_closer_look_files/figure-html/var.compare-1.png
docs/articles/flashier_intro.html
docs/articles/flashier_intro_files/figure-html/flash-point-normal-1.png
docs/articles/flashier_intro_files/figure-html/flash-snn-1.png
docs/articles/flashier_intro_files/figure-html/plot-flash-normal-1.png
docs/articles/flashier_intro_files/figure-html/tsne-1.png
docs/articles/flashier_single_cell.html
docs/articles/flashier_single_cell_files/figure-html/heatmap-1.png
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docs/articles/flashier_single_cell_files/figure-html/histograms-1.png
docs/articles/flashier_single_cell_files/figure-html/plot-change-vs-mean-1.png
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docs/articles/flashier_single_cell_files/figure-html/top-genes-all-1.png
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docs/articles/flashier_single_cell_files/figure-html/unnamed-chunk-8-1.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/figures/lifecycle-archived.svg
docs/reference/figures/lifecycle-defunct.svg
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docs/reference/figures/lifecycle-questioning.svg
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docs/reference/figures/lifecycle-stable.svg
docs/reference/figures/lifecycle-superseded.svg
docs/reference/fitted.flash.html
docs/reference/fitted.flash_fit.html
docs/reference/flash.html
docs/reference/flash_add_intercept.html
docs/reference/flash_backfit.html
docs/reference/flash_clear_timeout.html
docs/reference/flash_conv_crit_elbo_diff.html
docs/reference/flash_conv_crit_max_chg.html
docs/reference/flash_conv_crit_max_chg_F.html
docs/reference/flash_conv_crit_max_chg_L.html
docs/reference/flash_ebnm.html
docs/reference/flash_factors_fix.html
docs/reference/flash_factors_init.html
docs/reference/flash_factors_remove.html
docs/reference/flash_factors_reorder.html
docs/reference/flash_factors_set_to_zero.html
docs/reference/flash_factors_unfix.html
docs/reference/flash_fit.html
docs/reference/flash_greedy.html
docs/reference/flash_greedy_init_default.html
docs/reference/flash_greedy_init_irlba.html
docs/reference/flash_greedy_init_softImpute.html
docs/reference/flash_init.html
docs/reference/flash_nullcheck.html
docs/reference/flash_plot_bar-1.png
docs/reference/flash_plot_bar-2.png
docs/reference/flash_plot_bar.html
docs/reference/flash_plot_heatmap.html
docs/reference/flash_plot_histogram.html
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docs/reference/flash_plot_scree.html
docs/reference/flash_plot_structure.html
docs/reference/flash_set_conv_crit.html
docs/reference/flash_set_timeout.html
docs/reference/flash_set_verbose.html
docs/reference/flash_update_data.html
docs/reference/flash_verbose_elbo.html
docs/reference/flash_verbose_elbo_diff.html
docs/reference/flash_verbose_max_chg.html
docs/reference/flash_verbose_max_chg_F.html
docs/reference/flash_verbose_max_chg_L.html
docs/reference/gtex.html
docs/reference/gtex_colors-1.png
docs/reference/gtex_colors-2.png
docs/reference/gtex_colors.html
docs/reference/index.html
docs/reference/ldf.html
docs/reference/plot.flash.html
docs/reference/residuals.flash.html
docs/reference/residuals.flash_fit.html
docs/sitemap.xml
flashier.Rproj
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-soft-deprecated.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/fitted.flash.Rd
man/fitted.flash_fit.Rd
man/flash.Rd
man/flash_add_intercept.Rd
man/flash_backfit.Rd
man/flash_clear_timeout.Rd
man/flash_conv_crit_elbo_diff.Rd
man/flash_conv_crit_max_chg.Rd
man/flash_conv_crit_max_chg_F.Rd
man/flash_conv_crit_max_chg_L.Rd
man/flash_ebnm.Rd
man/flash_factors_fix.Rd
man/flash_factors_init.Rd
man/flash_factors_remove.Rd
man/flash_factors_reorder.Rd
man/flash_factors_set_to_zero.Rd
man/flash_factors_unfix.Rd
man/flash_fit.Rd
man/flash_greedy.Rd
man/flash_greedy_init_default.Rd
man/flash_greedy_init_irlba.Rd
man/flash_greedy_init_softImpute.Rd
man/flash_init.Rd
man/flash_nullcheck.Rd
man/flash_plot_bar.Rd
man/flash_plot_heatmap.Rd
man/flash_plot_histogram.Rd
man/flash_plot_scatter.Rd
man/flash_plot_scree.Rd
man/flash_plot_structure.Rd
man/flash_set_conv_crit.Rd
man/flash_set_timeout.Rd
man/flash_set_verbose.Rd
man/flash_update_data.Rd
man/flash_verbose_elbo.Rd
man/flash_verbose_elbo_diff.Rd
man/flash_verbose_max_chg.Rd
man/flash_verbose_max_chg_F.Rd
man/flash_verbose_max_chg_L.Rd
man/gtex.Rd
man/gtex_colors.Rd
man/ldf.Rd
man/plot.flash.Rd
man/residuals.flash.Rd
man/residuals.flash_fit.Rd
tests/testthat/test_dense_no_missing.R
tests/testthat/test_fixed_factors.R
tests/testthat/test_lowrank.R
tests/testthat/test_ops.R
tests/testthat/test_sparse_missing.R
tests/testthat/test_tensor.R
tests/testthat/test_var_types.R
vignettes/advanced_flashier.Rmd
vignettes/flashier.bib
vignettes/flashier_closer_look.Rmd
vignettes/flashier_intro.Rmd
vignettes/flashier_single_cell.Rmd
