Files in AllenInstitute/scrattch.hicat

Hierarchical Iterative Clustering Analysis for Transcriptomic data

R/CCA.R R/KNN.graph.R R/annotate.R R/cluster.R R/cluster_cv.R R/consensusCluster.R R/de.genes.R R/dend.markers.R R/dendro.R R/deprecated_function_names.R R/doubletFinder.R R/find_noise_cl.R R/harmonize.R R/harmonize_impute.R R/harmonize_merge.R R/harmonize_util.R R/heatmap.R R/heatmap4.R R/human_functions.R R/human_functions_rename.r R/map_to_dend.R R/markers.R R/merge_cl.R R/normalize.R R/plot.R R/reduceDimension_PCA.R R/reduceDimension_Umap.R R/reduceDimension_WGCNA.R R/reduceDimension_plot.R R/reduceDimension_tSNE.R R/util.R R/vg.R README.md data/Constellation_example/plot/20190920_1126_constellation.pdf data/Constellation_example/plot/20191001_0850_constellation.pdf data/Constellation_example/plot/20221028_152708_constellation.pdf man/CCA.Rd man/CanonCor.Rd man/DE_genes_cat_by_cl.Rd man/DE_genes_pairs.Rd man/DE_genes_pw.Rd man/RunUMAP.Rd man/adjust_color.Rd man/angle.Rd man/avgangle.Rd man/batch_process.Rd man/build_dend.Rd man/build_dend_harmonize.Rd man/build_dend_with_means.Rd man/build_tsne.Rd man/calc_tau.Rd man/check_donor.Rd man/check_neun.Rd man/check_outlier.Rd man/check_qc.Rd man/clean_outliers.Rd man/collect_co_matrix.Rd man/comb_de_result.Rd man/combine_cl.Rd man/compare_annotate.Rd man/compare_plot.Rd man/compute_knn.Rd man/compute_vg_stats.Rd man/convert_pair_matrix.Rd man/convert_pair_matrix_str.Rd man/cpm.Rd man/create_pairs.Rd man/cutree_dend.Rd man/de_all_pairs.Rd man/de_genes_pairs_multiple.Rd man/de_pair.Rd man/de_pair_chisq.Rd man/de_pair_limma.Rd man/de_param.Rd man/de_score.Rd man/de_score_pairs.Rd man/de_selected_pairs.Rd man/de_stats_all_pairs.Rd man/de_stats_pair.Rd man/de_stats_selected_pairs.Rd man/dend_lca.Rd man/dend_list.Rd man/dend_match.Rd man/display_cl.Rd man/display_cl4.Rd man/display_cl_markers_co.ratio.Rd man/display_cl_one_vs_others.Rd man/doubletFinder.Rd man/edgeMaker.Rd man/fast_tsne.Rd man/findVG.Rd man/find_doublet.Rd man/find_low_quality_cl.Rd man/find_vg.Rd man/gene_dispersion.Rd man/gene_gene_cor_conservation.Rd man/gene_loess_fit.Rd man/gene_loess_fit_z.Rd man/gene_means.Rd man/gene_vars.Rd man/gene_z.Rd man/get.markers.num.Rd man/getTopMarkersByPropNew.Rd man/get_RD_cl_center.Rd man/get_beta_score.Rd man/get_cell.cl.co.ratio.Rd man/get_cl_df.Rd man/get_cl_mat.Rd man/get_cl_means.Rd man/get_cl_means_list.Rd man/get_cl_medians.Rd man/get_cl_present_list.Rd man/get_cl_prop.Rd man/get_cl_sim.Rd man/get_cl_sim_multiple.Rd man/get_cl_sums.Rd man/get_core_intermediate.Rd man/get_de_genes_sym.Rd man/get_de_lfc_list.Rd man/get_de_matrix.Rd man/get_de_pair.Rd man/get_de_result.Rd man/get_de_score.Rd man/get_dend_markers.Rd man/get_dend_markers_direction.Rd man/get_dend_parent.Rd man/get_eigen.Rd man/get_gene_cl_correlation.Rd man/get_gene_score.Rd man/get_knn.Rd man/get_knn_batch.Rd man/get_knn_graph.Rd man/get_knn_weight.Rd man/get_pair_matrix.Rd man/get_pair_matrix_coor.Rd man/get_pairs.Rd man/group_cl.Rd man/group_specific_markers.Rd man/harmonize.Rd man/heatmap.3.Rd man/heatmap.4.Rd man/i_harmonize.Rd man/impute_knn.Rd man/impute_knn_global.Rd man/impute_val_cor.Rd man/incrementHex.Rd man/iter_clust.Rd man/iter_consensus_clust.Rd man/iter_impute_knn.Rd man/jaccard.Rd man/jaccard_leiden.RANN.Rd man/jaccard_leiden.Rd man/jaccard_louvain.RANN.Rd man/jaccard_louvain.Rd man/knn_cor.Rd man/knn_cosine.Rd man/knn_jaccard_louvain.Rd man/knn_joint.Rd man/label_dend.Rd man/lm_matrix.Rd man/lm_normalize.Rd man/logCPM.Rd man/makeColorsUnique.Rd man/makeLayerLabel.Rd man/makeRegionLabel.Rd man/map_by_cor.Rd man/map_cl_summary.Rd man/map_cv.Rd man/map_dend.Rd man/map_dend_markers.Rd man/map_dend_membership.Rd man/map_sampling.Rd man/mapping.Rd man/markers_max_tau.Rd man/markers_tau_one_vs_other.Rd man/match_cl.Rd man/merge_cl.Rd man/merge_cl_multiple.Rd man/merge_knn_result.Rd man/multiplot.Rd man/mybgplot3d.Rd man/node_specific_markers.Rd man/node_vs_sibling_markers.Rd man/onestep_clust.Rd man/pair_cor.Rd man/perp.Rd man/perpEnd.Rd man/perpMid.Rd man/perpStart.Rd man/plot_2d_select.Rd man/plot_3d_label.Rd man/plot_3d_label_multiple.Rd man/plot_3d_select.Rd man/plot_3d_val.Rd man/plot_RD_cl.Rd man/plot_RD_gene.Rd man/plot_RD_meta.Rd man/plot_cl_cells.Rd man/plot_cl_heatmap.Rd man/plot_cl_heatmap4.Rd man/plot_cl_low.Rd man/plot_cl_meta_barplot.Rd man/plot_confusion.Rd man/plot_de_lfc_num.Rd man/plot_de_num.Rd man/plot_dend.Rd man/plot_doublet.Rd man/plot_low_qc.Rd man/plot_markers.Rd man/plot_markers_cl_means.Rd man/plot_pair_matrix.Rd man/plot_tSNE_gene.Rd man/plot_tSNE_meta.Rd man/plot_tsne.Rd man/plot_tsne_cl.Rd man/plot_vg.Rd man/prcomp.irlba.Rd man/predict_annotate_cor.Rd man/predict_knn.Rd man/predict_knn_new.Rd man/prune_dend.Rd man/pvclust_show_signif_gradient.Rd man/rd_PCA.Rd man/refine_cl.Rd man/renameAndOrderClusters.Rd man/reorder_cl.Rd man/reorder_dend.Rd man/reorder_factor.Rd man/rescale_samples.Rd man/resolve_cl.Rd man/run_consensus_clust.Rd man/sample_cells.Rd man/sample_sets_list.Rd man/select_N_markers.Rd man/select_dend_markers.Rd man/select_joint_genes.Rd man/select_joint_markers.Rd man/select_markers.Rd man/select_markers_pair.Rd man/select_markers_pair_direction.Rd man/select_markers_pair_group.Rd man/select_node_specific_markers.Rd man/select_pos_dend_markers.Rd man/select_pos_markers.Rd man/set_pair_matrix.Rd man/sim_knn.Rd man/simple_dend.Rd man/sparse_cor.Rd man/summarize_cl.Rd man/test_knn.Rd man/test_merge.Rd man/unbranch_by_conf.Rd man/unbranch_by_length.Rd man/updateSampDat.Rd man/vec_chisq_test.Rd man/within_group_specific_markers.Rd tests/testthat.R tests/testthat/test-CCA.R tests/testthat/test-annotate.R tests/testthat/test-cluster.R tests/testthat/test-cluster_cv.R tests/testthat/test-consensusCluster.R tests/testthat/test-de.genes.R tests/testthat/test-dend.markers.R tests/testthat/test-dendro.R tests/testthat/test-doubletFinder.R tests/testthat/test-heatmap.R tests/testthat/test-heatmap4.R tests/testthat/test-markers.R tests/testthat/test-merge_cl.R tests/testthat/test-normalize.R tests/testthat/test-plot.R tests/testthat/test-reduceDimension_PCA.R tests/testthat/test-reduceDimension_WGCNA.R tests/testthat/test-reduceDimension_plot.R tests/testthat/test-reduceDimension_tSNE.R tests/testthat/test-riverplot.R tests/testthat/test-update.R tests/testthat/test-util.R tests/testthat/test-vg.R tests/testthat/test_human_functions.R vignettes/deprecated-scrattch.R vignettes/scrattch.hicat.R vignettes/scrattch.hicat_release.Rmd