Man pages for lakhanp1/chipmine
Analyze ChIP-seq Data
| add_annotation_titles | Add annotation column titles on the heatmap |
| best_replicate_peakset | Get good replicate's peakset from two or more ChIPseq... |
| bigwig_profile_matrix | Generate profile matrix using normalizeToMatrix() |
| chip_summary | TF ChIPseq data summary plots |
| combinatorial_binding_matrix | Generate the combinatorial peak association matrix with... |
| compare_ChIPseq_replicates | TF ChIPseq replicate correlation plots |
| compare_replicates | Correlation plots for numeric data |
| draw_avg_profile_plot | Average signal plot for multiple samples |
| gene_length_heatmap_annotation | Gene length annotation as points |
| geneset_average_profile | Calculate average profile for a gene list |
| get_expression_heatmap_list | Multiple PolII expression heatmaps as list |
| get_fold_change | Raw log2 fold change value between two samples as log2(s2/s1) |
| get_peak_summit_seq | Get DNA sequence from peak summit region |
| get_polII_expressions | PolII signal list from multiple samples |
| get_polII_signal | Read polII binding signal data for a sample |
| get_profile_plot_list | Multiple Enriched Heatmaps as list |
| get_sample_information | Create sample information dataframe |
| get_TES | Extract the TES position as GenomicRanges |
| get_TF_binding_data | Get the TF peak annotation data |
| get_txdb_exons_gr | Exons GRanges object from TxDB |
| get_txdb_fiveUtr_gr | 5UTR GRanges object from TxDB |
| get_txdb_introns_gr | Introns GRanges object from TxDB |
| get_txdb_threeUtr_gr | 3UTR GRanges object from TxDB |
| get_txdb_transcripts_gr | Transcripts GRanges object from TxDB |
| hello | Hello, World! |
| import_peaks_as_df | Read peak file as dataframe with selected columns |
| import_profile_from_file | Read profile matrix from file |
| import_profiles | Generate profile matrix list |
| merged_profile_matrix_cluster | Merged profile matrix clustering |
| multi_profile_plots | 'EnrichedHeatmap' plots and 'ComplexHeatmaps' for multiple... |
| na_impute | Replace NA values by row mean |
| peak_target_matrix | Peak target gene matrix for multiple samples |
| plot_MA_gg | Generate MA plot |
| plot_scatter | Generate XY scatter plot for two sets |
| preProcess_polII_expression | Pre-process polII expression data |
| profile_heatmap | Generate profile heatmap |
| profile_matrix_kmeans | Profile Matrix k-means Clustering |
| region_coverage | Calculate mean coverage for regions. |
| region_coverage_matrix | Coverage matrix for regions of interest |
| scale_matrix_columns | column wise z-score scaling of matrix |
| scale_matrix_rows | row wise z-score scaling of matrix |
| signal_heatmap | Heatmap for polII binding signal |
