Files in wmacnair/SampleQC
Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/RcppExports.R
R/SampleQC-package.R
R/SampleQC_utils.R
R/calc_pairwise_mmds.R
R/fit_sampleqc.R
R/get_outliers.R
R/make_qc_dt.R
R/make_sampleqc_report.R
R/plot_alpha_js.R
R/plot_alpha_js_likelihoods.R
R/plot_beta_ks.R
R/plot_embeddings.R
R/plot_fit_over_biaxials.R
R/plot_mmd_heatmap.R
R/plot_outliers.R
R/simulate_qcs.R
README.md
inst/Rmd/SampleQC_report_template.Rmd
man/SampleQC.Rd
man/calc_pairwise_mmds.Rd
man/dot-add_annot_vars.Rd
man/dot-add_log_counts.Rd
man/dot-add_log_feats.Rd
man/dot-add_logit_mito.Rd
man/dot-add_qc_annots.Rd
man/dot-add_splice_ratio.Rd
man/dot-add_unknown_metrics.Rd
man/dot-assemble_fit_results.Rd
man/dot-calc_ellipses_dt.Rd
man/dot-calc_mat_list.Rd
man/dot-calc_mmd_mat.Rd
man/dot-calc_one_ellipse.Rd
man/dot-calc_outliers_dt.Rd
man/dot-calc_p_jk_proportions.Rd
man/dot-check_fit_params.Rd
man/dot-check_is_qc_obj.Rd
man/dot-check_qc_dt.Rd
man/dot-cluster_mmd_graph.Rd
man/dot-dist_fn.Rd
man/dot-draw_Sigma_k.Rd
man/dot-draw_alpha_j.Rd
man/dot-draw_beta_k.Rd
man/dot-draw_delta_jk.Rd
man/dot-draw_dir_0.Rd
man/dot-draw_expt_params.Rd
man/dot-draw_mu_0s.Rd
man/dot-draw_out_j.Rd
man/dot-draw_outliers.Rd
man/dot-draw_p_jk.Rd
man/dot-draw_p_loss_0s.Rd
man/dot-draw_p_out_0s.Rd
man/dot-draw_samples.Rd
man/dot-draw_sel_ks.Rd
man/dot-draw_theta_0s.Rd
man/dot-draw_z.Rd
man/dot-embed_mds.Rd
man/dot-embed_umap.Rd
man/dot-fit_one_sampleqc.Rd
man/dot-init_clusts.Rd
man/dot-init_qc_dt.Rd
man/dot-make_mmd_graph.Rd
man/dot-make_toy_qc_df.Rd
man/dot-make_toy_sce.Rd
man/dot-plot_one_embedding.Rd
man/dot-process_annot_vars.Rd
man/dot-process_outputs.Rd
man/dot-sim_ok_cells.Rd
man/dot-sim_outliers.Rd
man/dot-sim_sample_group.Rd
man/fit_sampleqc.Rd
man/fit_sampleqc_mle_cpp.Rd
man/fit_sampleqc_robust_cpp.Rd
man/get_n_groups.Rd
man/get_outliers.Rd
man/list_known_metrics.Rd
man/make_qc_dt.Rd
man/make_sampleqc_report.Rd
man/mmd_fn.Rd
man/plot_alpha_js.Rd
man/plot_alpha_js_likelihoods.Rd
man/plot_beta_ks.Rd
man/plot_embeddings.Rd
man/plot_fit_over_biaxials.Rd
man/plot_mmd_heatmap.Rd
man/plot_outliers.Rd
man/simulate_qcs.Rd
man/subsample_mmd_fn.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/fit_sampleQC_mle_cpp.cpp
src/fit_sampleQC_robust_cpp.cpp
src/helpers.cpp
src/helpers.h
src/mmd_fn.cpp
src/subsample_mmd_fn.cpp
tests/testthat.R
tests/testthat/test-01_make_qc_dt.R
tests/testthat/test-02_calc_pairwise_mmds.R
tests/testthat/test-03_fit_sampleqc.R
tests/testthat/test-04_simulate_qcs.R
tests/testthat/test-05_utils.R
