Files in rnabioco/clustifyR

Classifier for Single-cell RNA-seq Using Cell Clusters

.github/CODE_OF_CONDUCT.md .github/CONTRIBUTING.md R/cellbrowsers.R R/clustifyR-package.R R/common_dplyr.R R/compare_genelist.R R/compute_similarity.R R/data.R R/globals.R R/main.R R/object_access.R R/plot.R R/run_fgsea.R R/shiny.R R/utils.R README.Rmd README.md data-raw/cbmc_m.R data-raw/cbmc_ref.R data-raw/downrefs.R data-raw/human_genes_10x.R data-raw/mouse_genes_10x.R data-raw/object_loc_lookup.R data-raw/pbmc_bulk_matrix.R data-raw/pbmc_markers.R data-raw/pbmc_markers_M3Drop.R data-raw/pbmc_matrix_small.R data-raw/pbmc_meta.R data-raw/pbmc_vargenes.R inst/scripts/dl_reactome_gene_sets.R inst/shinyapp/README.md inst/shinyapp/data/example-input/get-data.R inst/shinyapp/global.R inst/shinyapp/server.R inst/shinyapp/ui.R man/append_genes.Rd man/assess_rank_bias.Rd man/assign_ident.Rd man/average_clusters.Rd man/binarize_expr.Rd man/build_atlas.Rd man/calc_distance.Rd man/calc_similarity.Rd man/calculate_pathway_gsea.Rd man/call_consensus.Rd man/call_to_metadata.Rd man/cbmc_m.Rd man/cbmc_ref.Rd man/check_raw_counts.Rd man/clustify.Rd man/clustify_lists.Rd man/clustify_nudge.Rd man/clustifyr-package.Rd man/clustifyr_methods.Rd man/collapse_to_cluster.Rd man/compare_lists.Rd man/cor_to_call.Rd man/cor_to_call_rank.Rd man/cor_to_call_topn.Rd man/cosine.Rd man/downrefs.Rd man/downsample_matrix.Rd man/feature_select_PCA.Rd man/file_marker_parse.Rd man/find_rank_bias.Rd man/gene_pct.Rd man/gene_pct_markerm.Rd man/get_best_match_matrix.Rd man/get_best_str.Rd man/get_common_elements.Rd man/get_similarity.Rd man/get_ucsc_reference.Rd man/get_unique_column.Rd man/get_vargenes.Rd man/gmt_to_list.Rd man/human_genes_10x.Rd man/insert_meta_object.Rd man/kl_divergence.Rd man/make_comb_ref.Rd man/marker_select.Rd man/matrixize_markers.Rd man/mouse_genes_10x.Rd man/not_pretty_palette.Rd man/object_data.Rd man/object_loc_lookup.Rd man/object_ref.Rd man/overcluster.Rd man/overcluster_test.Rd man/parse_loc_object.Rd man/pbmc_markers.Rd man/pbmc_markers_M3Drop.Rd man/pbmc_matrix_small.Rd man/pbmc_meta.Rd man/pbmc_vargenes.Rd man/percent_clusters.Rd man/permute_similarity.Rd man/plot_best_call.Rd man/plot_call.Rd man/plot_cor.Rd man/plot_cor_heatmap.Rd man/plot_dims.Rd man/plot_gene.Rd man/plot_pathway_gsea.Rd man/plot_rank_bias.Rd man/pos_neg_marker.Rd man/pos_neg_select.Rd man/pretty_palette.Rd man/pretty_palette2.Rd man/pretty_palette_ramp_d.Rd man/query_rank_bias.Rd man/ref_feature_select.Rd man/ref_marker_select.Rd man/reverse_marker_matrix.Rd man/run_clustifyr_app.Rd man/run_gsea.Rd man/sce_pbmc.Rd man/seurat_meta.Rd man/seurat_ref.Rd man/so_pbmc.Rd man/vector_similarity.Rd man/write_meta.Rd tests/testthat.R tests/testthat/test_cor.R tests/testthat/test_gsea.R tests/testthat/test_list.R tests/testthat/test_plots.R tests/testthat/test_utils.R vignettes/clustifyr.Rmd vignettes/geo-annotations.Rmd