Files in tanaylab/metacell
Meta cell analysis for single cell RNA-seq data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/atlas.r
R/atlas_project.r
R/cgraph.r
R/cgraph_extmat.r
R/cgraph_gcor_norm.r
R/cgraph_knn.r
R/cgraph_knn_mcnorm.r
R/coclust.r
R/coclust_graph_cov.r
R/gene_names_xref_util.r
R/gset.r
R/gset_clust.r
R/gset_feat_select.r
R/gset_mc.r
R/gset_plot_mats.r
R/gstats.r
R/gstats_report.r
R/mc.r
R/mc2d.r
R/mc2d_force_knn.r
R/mc2d_plot.r
R/mc_apx_qc.r
R/mc_apx_qc_cv.r
R/mc_colorize.r
R/mc_confusion.r
R/mc_export_tab.r
R/mc_from_coclust.r
R/mc_graphcov.r
R/mc_hierarchy.r
R/mc_outliers.r
R/mc_plot_by_factor.r
R/mc_plot_confusion.r
R/mc_plot_cross_mc.r
R/mc_plot_marks.r
R/mc_plot_vgels.r
R/mctnetwork.r
R/mctnetwork_clust.r
R/mctnetwork_plot_net.r
R/metacell-package.r
R/mgraph.r
R/mgraph_knn.r
R/mgraph_logistic.r
R/mincost_flow.r
R/pipe_vanila.r
R/scdb.r
R/scfigs.r
R/scmat.r
R/scmat_10x.r
R/scmat_batch_stat.r
R/scmat_ccor.r
R/scmat_gcors.r
R/scmat_import.r
R/scmat_mars.r
R/stat_utils.r
R/utils-pipe.R
R/utils.r
R/zzz.r
README.Rmd
README.md
_pkgdown.yml
inst/config/metacell_params.yaml
inst/extdata/guo2018_marks.txt
inst/extdata/guo2018_mc_partial_colorize.txt
inst/extdata/guo2018_supmc.txt
inst/extdata/pbmc_mc_colorize.txt
man/allrow_cor.Rd
man/gen_10x_mars_gene_match.Rd
man/gset_add_genes.Rd
man/gset_get_feat_mat.Rd
man/gset_get_genes.Rd
man/gset_import_table.Rd
man/gset_new_gset.Rd
man/gset_new_restrict_gset.Rd
man/gset_new_restrict_nms.Rd
man/gset_write_table.Rd
man/initialize-tgCellGraph-method.Rd
man/initialize-tgCoClust-method.Rd
man/initialize-tgGeneSets-method.Rd
man/initialize-tgMC2D-method.Rd
man/initialize-tgMCAtlas-method.Rd
man/initialize-tgMCCov-method.Rd
man/initialize-tgMCManifGraph-method.Rd
man/initialize-tgMCTNetwork-method.Rd
man/mc_colorize.Rd
man/mc_colorize_default.Rd
man/mc_colorize_from_ref_mc.Rd
man/mc_colorize_sup_hierarchy.Rd
man/mc_compute_cov_gc.Rd
man/mc_compute_e_gc.Rd
man/mc_compute_fp.Rd
man/mc_compute_n_bc.Rd
man/mc_compute_outlier_fc.Rd
man/mc_reorder.Rd
man/mc_restrict.Rd
man/mc_set_outlier_mc.Rd
man/mc_update_stats.Rd
man/mcatlas_annotate_mc_by_mc2mc_projection.Rd
man/mcatlas_annotate_mc_by_sc2mc_projection.Rd
man/mcatlas_annotate_mc_by_sc2sc_projection.Rd
man/mcatlas_comp_adj_type_n.Rd
man/mcatlas_project_query.Rd
man/mcell_add_cgraph_bknn_norm_mc.Rd
man/mcell_add_cgraph_from_distmat.Rd
man/mcell_add_cgraph_from_mat_bknn.Rd
man/mcell_add_cgraph_from_mat_raw_knn.Rd
man/mcell_add_gene_names_xref_mars10x.Rd
man/mcell_add_gene_stat.Rd
man/mcell_add_mars_facs_data.Rd
man/mcell_add_mc_from_graph.Rd
man/mcell_batch_stats.Rd
man/mcell_calc_one_batch_stats.Rd
man/mcell_cgraph_norm_gcor.Rd
man/mcell_coclust_filt_by_k_deg.Rd
man/mcell_coclust_from_graph_resamp.Rd
man/mcell_compare_bulk.Rd
man/mcell_gen_atlas.Rd
man/mcell_gen_cell_cor_gset.Rd
man/mcell_graph_pred_corr.Rd
man/mcell_gset_add_gene.Rd
man/mcell_gset_filter_cov.Rd
man/mcell_gset_filter_multi.Rd
man/mcell_gset_filter_szcor.Rd
man/mcell_gset_filter_varmean.Rd
man/mcell_gset_from_mc_markers.Rd
man/mcell_gset_remove_clusts.Rd
man/mcell_gset_split_by_dsmat.Rd
man/mcell_import_multi_mars.Rd
man/mcell_import_multi_scmat_10x.Rd
man/mcell_import_scmat_10x.Rd
man/mcell_import_scmat_tsv.Rd
man/mcell_mat_ignore_cells.Rd
man/mcell_mat_ignore_genes.Rd
man/mcell_mat_ignore_small_cells.Rd
man/mcell_mat_rpt_cor_anchors.Rd
man/mcell_mc2d_force_knn.Rd
man/mcell_mc2d_force_knn_on_cells.Rd
man/mcell_mc2d_plot.Rd
man/mcell_mc2d_plot_by_factor.Rd
man/mcell_mc2d_plot_gene.Rd
man/mcell_mc2d_rotate.Rd
man/mcell_mc_add_annot.Rd
man/mcell_mc_add_color.Rd
man/mcell_mc_cell_homogeneity.Rd
man/mcell_mc_coclust_confusion_mat.Rd
man/mcell_mc_confusion_mat.Rd
man/mcell_mc_edge_density.Rd
man/mcell_mc_export_tab.Rd
man/mcell_mc_from_coclust_balanced.Rd
man/mcell_mc_from_coclust_hc.Rd
man/mcell_mc_from_coclust_louv_sub.Rd
man/mcell_mc_hclust_confu.Rd
man/mcell_mc_hierarchy.Rd
man/mcell_mc_match_graph.Rd
man/mcell_mc_plot_by_factor.Rd
man/mcell_mc_plot_confusion.Rd
man/mcell_mc_plot_gg.Rd
man/mcell_mc_plot_hierarchy.Rd
man/mcell_mc_plot_marks.Rd
man/mcell_mc_plot_submc_marks.Rd
man/mcell_mc_plot_vgels.Rd
man/mcell_mc_pred_corr.Rd
man/mcell_mc_reorder_hc.Rd
man/mcell_mc_screen_outliers_1gene_fold.Rd
man/mcell_mc_split_by_color_group.Rd
man/mcell_mc_split_filt.Rd
man/mcell_merge_mats.Rd
man/mcell_mgraph_knn.Rd
man/mcell_mgraph_logistic.Rd
man/mcell_new_mc.Rd
man/mcell_new_mc2d.Rd
man/mcell_new_mc_mgraph.Rd
man/mcell_new_mcatlas.Rd
man/mcell_new_mctnetwork.Rd
man/mcell_pipe_mat2mc2d.Rd
man/mcell_plot_batch_stats.Rd
man/mcell_plot_cross_mc.Rd
man/mcell_plot_gset_cor_mats.Rd
man/mcell_plot_gstats.Rd
man/mcell_plot_outlier_heatmap.Rd
man/mcell_plot_umis_per_cell.Rd
man/mcell_proj_on_atlas.Rd
man/mcell_read_multi_scmat_10x.Rd
man/mcell_read_multi_scmat_mars.Rd
man/mcell_scmat_plot_cmp_kcor.Rd
man/mcell_wgtmc_pred_corr.Rd
man/mctnetwork_clust_flows.Rd
man/mctnetwork_comp_manifold_costs.Rd
man/mctnetwork_comp_propagation.Rd
man/mctnetwork_gen_e_gmt_p.Rd
man/mctnetwork_gen_gmod_mc_t.Rd
man/mctnetwork_gen_mincost_flows.Rd
man/mctnetwork_gen_network.Rd
man/mctnetwork_get_flow_mat.Rd
man/mctnetwork_get_type_flows.Rd
man/mctnetwork_propogate_from_t.Rd
man/metacell.Rd
man/pipe.Rd
man/plot_color_bar.Rd
man/port_cor.Rd
man/rescale_sparse_mat_cols.Rd
man/scdb_add_cgraph.Rd
man/scdb_add_coclust.Rd
man/scdb_add_gene_names_xref.Rd
man/scdb_add_gset.Rd
man/scdb_add_gstat.Rd
man/scdb_add_mat.Rd
man/scdb_add_mc.Rd
man/scdb_add_mc2d.Rd
man/scdb_add_mcatlas.Rd
man/scdb_add_mctnetwork.Rd
man/scdb_add_mgraph.Rd
man/scdb_cgraph.Rd
man/scdb_coclust.Rd
man/scdb_del_cgraph.Rd
man/scdb_del_coclust.Rd
man/scdb_del_gene_names_xref.Rd
man/scdb_del_gset.Rd
man/scdb_del_gstat.Rd
man/scdb_del_mat.Rd
man/scdb_del_mc.Rd
man/scdb_del_mc2d.Rd
man/scdb_del_mcatlas.Rd
man/scdb_del_mctnetwork.Rd
man/scdb_del_mgraph.Rd
man/scdb_gene_names_xref.Rd
man/scdb_gset.Rd
man/scdb_gstat.Rd
man/scdb_init.Rd
man/scdb_is_valid.Rd
man/scdb_ls.Rd
man/scdb_ls_loaded.Rd
man/scdb_mat.Rd
man/scdb_mc.Rd
man/scdb_mc2d.Rd
man/scdb_mcatlas.Rd
man/scdb_mctnetwork.Rd
man/scdb_mgraph.Rd
man/scfigs_dir.Rd
man/scfigs_fn.Rd
man/scfigs_init.Rd
man/scm_add_mars_facs_data.Rd
man/scm_downsamp.Rd
man/scm_export_mat_to_sce.Rd
man/scm_gene_stat.Rd
man/scm_ignore_cells.Rd
man/scm_ignore_genes.Rd
man/scm_import_sce_to_mat.Rd
man/scm_merge_mats.Rd
man/scm_new_matrix.Rd
man/scm_sub_mat.Rd
man/scm_which_downsamp_n.Rd
man/scmat_read_scmat_10x.Rd
man/scmat_read_scmat_10x_custom.Rd
man/tgCellGraph-class.Rd
man/tgCoClust-class.Rd
man/tgGeneSets-class.Rd
man/tgMC2D-class.Rd
man/tgMCAtlas-class.Rd
man/tgMCCov-class.Rd
man/tgMCManifGraph-class.Rd
man/tgMCTNetwork-class.Rd
man/tgScMat-class.Rd
man/tgs_cor_graph.Rd
metacell.Rproj
vignettes/a-basic_pbmc8k.Rmd
vignettes/b-geneset_by_anchor_pbmc8k.Rmd
vignettes/c-metacell_annotation.Rmd
vignettes/d-amphimedon.Rmd
vignettes/e-data_convert.Rmd
