API for ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App
| Global functions | |
|---|---|
| .onLoad | Source code |
| CompareWilcox | Man page Source code |
| CompareedgeRGLM | Man page Source code |
| DA_one_vs_rest_fun | 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 |
| bams_to_matrix_indexes | Man page Source code |
| beds_to_matrix_indexes | Man page Source code |
| call_macs2_merge_peaks | Man page Source code |
| 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 |
| consensus_clustering_scExp | Man page Source code |
| correlation_and_hierarchical_clust_scExp | 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_analysis_scExp | Man page Source code |
| distPearson | 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 |
| gene_set_enrichment_analysis_scExp | Man page Source code |
| generate_count_matrix | Man page Source code |
| generate_feature_names | Man page Source code |
| get_color_dataframe_from_input | Man page Source code |
| get_genomic_coordinates | 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 |
| 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 |
| 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 |
| 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 |
| peaks_to_bins | Man page Source code |
| plot_cluster_consensus_scExp | Man page Source code |
| plot_differential_H1_scExp | 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_heatmap_scExp | Man page Source code |
| plot_reduced_dim_scExp | Man page Source code |
| preprocess_CPM | Man page Source code |
| preprocess_RPKM | Man page Source code |
| preprocess_TPM | Man page Source code |
| preprocess_feature_size_only | Man page Source code |
| raw_counts_to_feature_count_files | Man page Source code |
| read_count_mat_with_separated_chr_start_end | 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 |
| 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 |
| subsample_scExp | Man page Source code |
| subset_bam_call_peaks | Man page 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_feature_count_files | Man page Source code |
