| annotation_from_merged_peaks | Find nearest peaks of each gene and return refined annotation |
| annotToCol2 | annotToCol2 |
| anocol_binary | Helper binary column for anocol function |
| anocol_categorical | Helper binary column for anocol function |
| bams_to_matrix_indexes | Count bam files on interval to create count indexes |
| beds_to_matrix_indexes | Count bed files on interval to create count indexes |
| calculate_CNA | Estimate copy number alterations in cytobands |
| calculate_cyto_mat | Calculate Fraction of reads in each cytobands |
| calculate_gain_or_loss | Estimate the copy gains/loss of tumor vs normal based on... |
| calculate_logRatio_CNA | Calculate the log2-ratio of tumor vs normal fraction of reads... |
| call_macs2_merge_peaks | Calling MACS2 peak caller and merging resulting peaks |
| ce11.chromosomes | Data.frame of chromosome length - ce11 |
| ce11.GeneTSS | Data.frame of gene TSS - ce11 |
| changeRange | changeRange |
| CheA3_TF_nTargets | A data.frame with the number of targets of each TF in ChEA3 |
| check_correct_datamatrix | Check if matrix rownames are well formated and correct if... |
| choose_cluster_scExp | Choose a number of clusters |
| choose_perplexity | Choose perplexity depending on number of cells for Tsne |
| col2hex | Col2Hex |
| colors_scExp | Adding colors to cells & features |
| combine_datamatrix | Combine two matrices and emit warning if no regions are in... |
| combine_enrichmentTests | Run enrichment tests and combine into list |
| comparable_variables | Find comparable variable scExp |
| CompareedgeRGLM | Creates a summary table with the number of genes under- or... |
| CompareWilcox | CompareWilcox |
| concatenate_scBed_into_clusters | Concatenate single-cell BED into clusters |
| consensus_clustering_scExp | Wrapper to apply ConsensusClusterPlus to scExp object |
| correlation_and_hierarchical_clust_scExp | Correlation and hierarchical clustering |
| count_coverage | Create a smoothed and normalized coverage track from a BAM... |
| create_project_folder | Create ChromSCape project folder |
| create_sample_name_mat | Create a sample name matrix |
| create_scDataset_raw | Create a simulated single cell datamatrix & cell annotation |
| create_scExp | Wrapper to create the single cell experiment from count... |
| DA_custom | Differential Analysis Custom in 'One vs One' mode |
| DA_one_vs_rest | Differential Analysis in 'One vs Rest' mode |
| DA_pairwise | Run differential analysis in Pairwise mode |
| define_feature | Define the features on which reads will be counted |
| detect_samples | Heuristic discovery of samples based on cell labels |
| differential_activation | Find Differentialy Activated Features (One vs All) |
| differential_analysis_scExp | Runs differential analysis between cell clusters |
| distPearson | distPearson |
| enrichmentTest | enrichmentTest |
| enrich_TF_ChEA3_genes | Find the TF that are enriched in the differential genes using... |
| enrich_TF_ChEA3_scExp | Find the TF that are enriched in the differential genes using... |
| exclude_features_scExp | Remove specific features (CNA, repeats) |
| feature_annotation_scExp | Add gene annotations to features |
| filter_correlated_cell_scExp | Filter lowly correlated cells |
| filter_genes_with_refined_peak_annotation | Filter genes based on peak calling refined annotation |
| filter_scExp | Filter cells and features |
| find_clusters_louvain_scExp | Build SNN graph and find cluster using Louvain Algorithm |
| find_top_features | Find most covered features |
| generate_analysis | Generate a complete ChromSCape analysis |
| generate_count_matrix | Generate count matrix |
| generate_coverage_tracks | Generate cell cluster pseudo-bulk coverage tracks |
| generate_feature_names | Generate feature names |
| generate_report | From a ChromSCape analysis directory, generate an HTML... |
| gene_set_enrichment_analysis_scExp | Runs Gene Set Enrichment Analysis on genes associated with... |
| get_color_dataframe_from_input | Get color dataframe from shiny::colorInput |
| get_cyto_features | Map features onto cytobands |
| getExperimentNames | Get experiment names from a SingleCellExperiment |
| get_genomic_coordinates | Get SingleCellExperiment's genomic coordinates |
| getMainExperiment | Get Main experiment of a SingleCellExperiment |
| get_most_variable_cyto | Retrieve the cytobands with the most variable fraction of... |
| get_pathway_mat_scExp | Get pathway matrix |
| gg_fill_hue | gg_fill_hue |
| groupMat | groupMat |
| H1proportion | H1proportion |
| has_genomic_coordinates | Does SingleCellExperiment has genomic coordinates in features... |
| hclustAnnotHeatmapPlot | hclustAnnotHeatmapPlot |
| hg38.chromosomes | Data.frame of chromosome length - hg38 |
| hg38.cytoBand | Data.frame of cytoBandlocation - hg38 |
| hg38.GeneTSS | Data.frame of gene TSS - hg38 |
| imageCol | imageCol |
| import_count_input_files | Import and count input files depending on their format |
| import_scExp | Read single-cell matrix(ces) into scExp |
| index_peaks_barcodes_to_matrix_indexes | Read index-peaks-barcodes trio files on interval to create... |
| inter_correlation_scExp | Calculate inter correlation between cluster or samples |
| intra_correlation_scExp | Calculate intra correlation between cluster or samples |
| launchApp | Launch ChromSCape |
| load_MSIGdb | Load and format MSIGdb pathways using msigdbr package |
| merge_MACS2_peaks | Merge peak files from MACS2 peak caller |
| mm10.chromosomes | Data.frame of chromosome length - mm10 |
| mm10.cytoBand | Data.frame of cytoBandlocation - mm10 |
| mm10.GeneTSS | Data.frame of gene TSS - mm10 |
| normalize_scExp | Normalize counts |
| num_cell_after_cor_filt_scExp | Number of cells before & after correlation filtering |
| num_cell_after_QC_filt_scExp | Table of cells before / after QC |
| num_cell_before_cor_filt_scExp | Table of number of cells before correlation filtering |
| num_cell_in_cluster_scExp | Number of cells in each cluster |
| num_cell_scExp | Table of cells |
| pca_irlba_for_sparseMatrix | Run sparse PCA using irlba SVD |
| plot_cluster_consensus_scExp | Plot cluster consensus |
| plot_correlation_PCA_scExp | Plotting correlation of PCs with a variable of interest |
| plot_coverage_BigWig | Coverage plot |
| plot_differential_summary_scExp | Differential summary barplot |
| plot_differential_volcano_scExp | Volcano plot of differential features |
| plot_distribution_scExp | Plotting distribution of signal |
| plot_gain_or_loss_barplots | Plot Gain or Loss of cytobands of the most variables... |
| plot_heatmap_scExp | Plot cell correlation heatmap with annotations |
| plot_inter_correlation_scExp | Violin plot of inter-correlation distribution between one or... |
| plot_intra_correlation_scExp | Violin plot of intra-correlation distribution |
| plot_most_contributing_features | Plot Top/Bottom most contributing features to PCA |
| plot_percent_active_feature_scExp | Barplot of the % of active cells for a given features |
| plot_pie_most_contributing_chr | Pie chart of top contribution of chromosomes in the 100 most... |
| plot_reduced_dim_scExp | Plot reduced dimensions (PCA, TSNE, UMAP) |
| plot_reduced_dim_scExp_CNA | Plot UMAP colored by Gain or Loss of cytobands |
| plot_top_TF_scExp | Barplot of top TFs from ChEA3 TF enrichment analysis |
| plot_violin_feature_scExp | Violin plot of features |
| preprocess_CPM | Preprocess scExp - Counts Per Million (CPM) |
| preprocess_feature_size_only | Preprocess scExp - size only |
| preprocessing_filtering_and_reduction | Preprocess and filter matrix annotation data project folder... |
| preprocess_RPKM | Preprocess scExp - Read per Kilobase Per Million (RPKM) |
| preprocess_TFIDF | Preprocess scExp - TF-IDF |
| preprocess_TPM | Preprocess scExp - Transcripts per Million (TPM) |
| raw_counts_to_sparse_matrix | Create a sparse count matrix from various format of input... |
| rawfile_ToBigWig | rawfile_ToBigWig : reads in BAM file and write out BigWig... |
| read_count_mat_with_separated_chr_start_end | Read a count matrix with three first columns (chr,start,end) |
| read_sparse_matrix | Read in one or multiple sparse matrices (10X format) |
| rebin_helper | Rebin Helper for rebin_matrix function |
| rebin_matrix | Transforms a bins x cells count matrix into a larger bins x... |
| reduce_dim_batch_correction | Reduce dimension with batch corrections |
| reduce_dims_scExp | Reduce dimensions (PCA, TSNE, UMAP) |
| remove_chr_M_fun | Remove chromosome M from scExprownames |
| remove_non_canonical_fun | Remove non canonical chromosomes from scExp |
| results_enrichmentTest | Resutls of hypergeometric gene set enrichment test |
| retrieve_top_bot_features_pca | Retrieve Top and Bot most contributing features of PCA |
| run_pairwise_tests | Run pairwise tests |
| run_tsne_scExp | Run tsne on single cell experiment |
| scExp | A SingleCellExperiment outputed by ChromSCape |
| separate_BAM_into_clusters | Separate BAM files into cell cluster BAM files |
| separator_count_mat | Determine Count matrix separator ("tab" or ",") |
| smoothBin | Smooth a vector of values with nb_bins left and righ values |
| subsample_scExp | Subsample scExp |
| subset_bam_call_peaks | Peak calling on cell clusters |
| summary_DA | Summary of the differential analysis |
| swapAltExp_sameColData | Swap main & alternative Experiments, with fixed colData |
| table_enriched_genes_scExp | Creates table of enriched genes sets |
| warning_DA | Warning for differential_analysis_scExp |
| warning_filter_correlated_cell_scExp | warning_filter_correlated_cell_scExp |
| warning_plot_reduced_dim_scExp | A warning helper for plot_reduced_dim_scExp |
| warning_raw_counts_to_sparse_matrix | Warning for raw_counts_to_sparse_matrix |
| wrapper_Signac_FeatureMatrix | Wrapper around 'FeatureMatrix' function from Signac Package |
