Analysis of single-cell epigenomics datasets with a Shiny App
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Documentation for package ‘ChromSCape’ version 1.4.0
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A B C D E F G H I L M N P R S T W
-- A --
| 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 |
-- B --
| 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 |
-- C --
| 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 log2-ratio of fraction of reads |
| calculate_logRatio_CNA | Calculate the log2-ratio of tumor vs normal fraction of reads in cytobands |
| call_macs2_merge_peaks | Calling MACS2 peak caller and merging resulting peaks |
| changeRange | changeRange |
| check_correct_datamatrix | Check if matrix rownames are well formated and correct if needed |
| 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 common |
| combine_enrichmentTests | Run enrichment tests and combine into list |
| CompareedgeRGLM | Creates a summary table with the number of genes under- or overexpressed in each group and outputs several graphical representations |
| 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 file and given a bin GenomicRanges object (same as deepTools bamCoverage) |
| 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 matrix and feature dataframe |
-- D --
| DA_custom | Differential Analysis in 'One vs Rest' mode |
| DA_one_vs_rest_fun | 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_analysis_scExp | Runs differential analysis between cell clusters |
| distPearson | distPearson |
-- E --
| enrichmentTest | enrichmentTest |
| exclude_features_scExp | Remove specific features (CNA, repeats) |
-- F --
| 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_top_features | Find most covered features |
-- G --
| 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 |
| gene_set_enrichment_analysis_scExp | Runs Gene Set Enrichment Analysis on genes associated with differential features |
| getExperimentNames | Get experiment names from a SingleCellExperiment |
| getMainExperiment | Get Main experiment of a SingleCellExperiment |
| get_color_dataframe_from_input | Get color dataframe from shiny::colorInput |
| get_cyto_features | Map features onto cytobands |
| get_genomic_coordinates | Get SingleCellExperiment's genomic coordinates |
| get_most_variable_cyto | Retrieve the cytobands with the most variable fraction of reads |
| gg_fill_hue | gg_fill_hue |
| groupMat | groupMat |
-- H --
| 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 |
-- I --
| 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 count indexes |
| inter_correlation_scExp | Calculate inter correlation between cluster or samples |
| intra_correlation_scExp | Calculate intra correlation between cluster or samples |
-- L --
| launchApp | Launch ChromSCape |
| load_MSIGdb | Load and format MSIGdb pathways using msigdbr package |
-- M --
| 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 |
-- N --
| 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 |
-- P --
| pca_irlba_for_sparseMatrix | Run sparse PCA using irlba SVD |
| peaks_to_bins | Transforms a peaks x cells count matrix into a bins x cells count matrix. |
| plot_cluster_consensus_scExp | Plot cluster consensus |
| plot_coverage_BigWig | Coverage plot using Sushi |
| plot_differential_H1_scExp | Differential H1 distribution 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 cytobands |
| plot_heatmap_scExp | Plot cell correlation heatmap with annotations |
| plot_inter_correlation_scExp | Violin plot of inter-correlation distribution between one or multiple groups and one reference group |
| plot_intra_correlation_scExp | Violin plot of intra-correlation distribution |
| plot_most_contributing_features | Plot Top/Bottom most contributing features to PCA |
| plot_pie_most_contributing_chr | Pie chart of top contribution of chromosomes in the 100 most contributing features to PCA #' |
| plot_reduced_dim_scExp | Plot reduced dimensions (PCA, TSNE, UMAP) |
| plot_reduced_dim_scExp_CNA | Plot UMAP colored by Gain or Loss of cytobands |
| preprocess_CPM | Preprocess scExp - Counts Per Million (CPM) |
| preprocess_feature_size_only | Preprocess scExp - size only |
| preprocess_RPKM | Preprocess scExp - Read per Kilobase Per Million (RPKM) |
| preprocess_TFIDF | Preprocess scExp - TF-IDF |
| preprocess_TPM | Preprocess scExp - Transcripts per Million (TPM) |
-- R --
| rawfile_ToBigWig | rawfile_ToBigWig : reads in BAM file and write out BigWig coverage file, normalized and smoothed |
| raw_counts_to_sparse_matrix | Create a sparse count matrix from various format of input data. |
| 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) |
| reduce_dims_scExp | Reduce dimensions (PCA, TSNE, UMAP) |
| reduce_dim_batch_correction | Reduce dimension with batch corrections |
| 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 |
-- S --
| 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 |
| swapAltExp_sameColData | Swap main & alternative Experiments, with fixed colData |
-- T --
| table_enriched_genes_scExp | Creates table of enriched genes sets |
-- W --
| 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 |