API for vallotlab/ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App
| Global functions | |
|---|---|
| .onLoad | Source code |
| CheA3_TF_nTargets | Man page |
| CompareWilcox | Man page Source code |
| CompareedgeRGLM | Man page Source code |
| DA_custom | Man page Source code |
| DA_one_vs_rest | Man page Source code |
| DA_pairwise | Man page Source code |
| H1proportion | Man page Source code |
| annotToCol2 | Man page Source code |
| annotation_from_merged_peaks | Man page Source code |
| anocol_binary | Man page Source code |
| anocol_categorical | Man page Source code |
| as_dist | Source code |
| bams_to_matrix_indexes | Man page Source code |
| beds_to_matrix_indexes | Man page Source code |
| calculate_CNA | Man page Source code |
| calculate_cyto_mat | Man page Source code |
| calculate_gain_or_loss | Man page Source code |
| calculate_logRatio_CNA | Man page Source code |
| call_macs2_merge_peaks | Man page Source code |
| ce11.GeneTSS | Man page |
| ce11.chromosomes | Man page |
| changeRange | Man page Source code |
| check_correct_datamatrix | Man page Source code |
| choose_cluster_scExp | Man page Source code |
| choose_perplexity | Man page Source code |
| col2hex | Man page Source code |
| colors_scExp | Man page Source code |
| combine_datamatrix | Man page Source code |
| combine_enrichmentTests | Man page Source code |
| comparable_variables | Man page Source code |
| concatenate_scBed_into_clusters | Man page Source code |
| consensus_clustering_scExp | Man page Source code |
| correlation_and_hierarchical_clust_scExp | Man page Source code |
| count_coverage | Man page Source code |
| create_project_folder | Man page Source code |
| create_sample_name_mat | Man page Source code |
| create_scDataset_raw | Man page Source code |
| create_scExp | Man page Source code |
| define_feature | Man page Source code |
| detect_samples | Man page Source code |
| differential_activation | Man page Source code |
| differential_analysis_scExp | Man page Source code |
| distPearson | Man page Source code |
| enrich_TF_ChEA3_genes | Man page Source code |
| enrich_TF_ChEA3_scExp | Man page Source code |
| enrichmentTest | Man page Source code |
| exclude_features_scExp | Man page Source code |
| feature_annotation_scExp | Man page Source code |
| filter_correlated_cell_scExp | Man page Source code |
| filter_genes_with_refined_peak_annotation | Man page Source code |
| filter_scExp | Man page |
| find_clusters_louvain_scExp | Man page Source code |
| find_top_features | Man page |
| gene_set_enrichment_analysis_scExp | Man page Source code |
| generate_analysis | Man page Source code |
| generate_count_matrix | Man page Source code |
| generate_coverage_tracks | Man page Source code |
| generate_feature_names | Man page Source code |
| generate_report | Man page Source code |
| getExperimentNames | Man page Source code |
| getMainExperiment | Man page Source code |
| get_color_dataframe_from_input | Man page Source code |
| get_cyto_features | Man page Source code |
| get_genomic_coordinates | Man page Source code |
| get_most_variable_cyto | Man page Source code |
| get_pathway_mat_scExp | Man page Source code |
| gg_fill_hue | Man page Source code |
| groupMat | Man page Source code |
| has_genomic_coordinates | Man page Source code |
| hclustAnnotHeatmapPlot | Man page Source code |
| hg38.GeneTSS | Man page |
| hg38.chromosomes | Man page |
| hg38.cytoBand | Man page |
| imageCol | Man page Source code |
| import_count_input_files | Man page Source code |
| import_scExp | Man page Source code |
| index_peaks_barcodes_to_matrix_indexes | Man page Source code |
| inter_correlation_scExp | Man page Source code |
| intra_correlation_scExp | Man page Source code |
| launchApp | Man page Source code |
| load_MSIGdb | Man page Source code |
| merge_MACS2_peaks | Man page Source code |
| mm10.GeneTSS | Man page |
| mm10.chromosomes | Man page |
| mm10.cytoBand | Man page |
| normalize_scExp | Man page Source code |
| num_cell_after_QC_filt_scExp | Man page Source code |
| num_cell_after_cor_filt_scExp | Man page Source code |
| num_cell_before_cor_filt_scExp | Man page Source code |
| num_cell_in_cluster_scExp | Man page Source code |
| num_cell_scExp | Man page Source code |
| pca_irlba_for_sparseMatrix | Man page Source code |
| plot_cluster_consensus_scExp | Man page Source code |
| plot_correlation_PCA_scExp | Man page Source code |
| plot_coverage_BigWig | Man page Source code |
| plot_differential_summary_scExp | Man page Source code |
| plot_differential_volcano_scExp | Man page Source code |
| plot_distribution_scExp | Man page Source code |
| plot_gain_or_loss_barplots | Man page Source code Source code |
| plot_heatmap_scExp | Man page Source code |
| plot_inter_correlation_scExp | Man page Source code |
| plot_intra_correlation_scExp | Man page Source code |
| plot_most_contributing_features | Man page Source code |
| plot_percent_active_feature_scExp | Man page Source code |
| plot_pie_most_contributing_chr | Man page Source code |
| plot_reduced_dim_scExp | Man page Source code |
| plot_reduced_dim_scExp_CNA | Man page Source code |
| plot_top_TF_scExp | Man page Source code |
| plot_violin_feature_scExp | Man page Source code |
| preprocess_CPM | Man page Source code |
| preprocess_RPKM | Man page Source code |
| preprocess_TFIDF | Man page Source code |
| preprocess_TPM | Man page Source code |
| preprocess_feature_size_only | Man page Source code |
| preprocessing_filtering_and_reduction | Man page Source code |
| rawData_to_datamatrix_annot | Source code |
| raw_counts_to_sparse_matrix | Man page Source code |
| rawfile_ToBigWig | Man page Source code |
| read_count_mat_with_separated_chr_start_end | Man page Source code |
| read_sparse_matrix | Man page Source code |
| rebin_helper | Man page Source code |
| rebin_matrix | Man page Source code |
| reduce_dim_batch_correction | Man page Source code |
| reduce_dims_scExp | Man page Source code |
| remove_chr_M_fun | Man page Source code |
| remove_non_canonical_fun | Man page Source code |
| results_enrichmentTest | Man page Source code |
| retrieve_top_bot_features_pca | Man page Source code |
| run_pairwise_tests | Man page Source code |
| run_tsne_scExp | Man page Source code |
| scExp | Man page |
| separate_BAM_into_clusters | Man page Source code |
| separator_count_mat | Man page Source code |
| set_ChromSCape_options | Source code |
| smoothBin | Man page Source code |
| subsample_scExp | Man page Source code |
| subset_bam_call_peaks | Man page Source code |
| summary_DA | Man page Source code |
| swapAltExp_sameColData | Man page Source code |
| sweep_sparse | Source code |
| table_enriched_genes_scExp | Man page Source code |
| warning_DA | Man page Source code |
| warning_filter_correlated_cell_scExp | Man page Source code |
| warning_plot_reduced_dim_scExp | Man page Source code |
| warning_raw_counts_to_sparse_matrix | Man page Source code |
| wrapper_Signac_FeatureMatrix | Man page Source code |
