Plot profiles of next generation sequencing data in genomic
features
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Documentation for package ‘GenomicPlot’ version 1.7.2
Help Pages
| aov_TukeyHSD | Perform one-way ANOVA and post hoc TukeyHSD tests |
| check_constraints | Check constraints of genomic ranges |
| chip_input_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package |
| chip_treat_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package |
| custom_TxDb_from_GTF | Make custom TxDb object from a GTF/GFF file |
| draw_boxplot_by_factor | Plot boxplot with two factors |
| draw_boxplot_wo_outlier | Plot boxplot without outliers |
| draw_combo_plot | Make combo plot for statistics plots |
| draw_locus_profile | Plot signal profile around genomic loci |
| draw_matrix_heatmap | Display matrix as a heatmap |
| draw_mean_se_barplot | Plot barplot for mean with standard error bars |
| draw_quantile_plot | Plot quantile over value |
| draw_rank_plot | Plot fraction of cumulative sum over rank |
| draw_region_landmark | Plot genomic region landmark indicator |
| draw_region_name | Plot genomic region names |
| draw_region_profile | Plot signal profile in genomic regions |
| draw_stacked_plot | draw stacked plot |
| draw_stacked_profile | Plot signal profile around start, center, and end of genomic regions |
| effective_size | Normalize sample library size to effective size |
| extdata | Toy data for examples and testing of the 'GenomicPlot' package |
| extract_longest_tx | Extract the longest transcript for each protein-coding genes |
| filter_by_nonoverlaps_stranded | Filter GRanges by nonoverlaps in a stranded way |
| filter_by_overlaps_nonstranded | Filter GRanges by overlaps in a nonstranded way |
| filter_by_overlaps_stranded | Filter GRanges by overlaps in a stranded way |
| gencode.v19.annotation_chr19.gtf | Toy data for examples and testing of the 'GenomicPlot' package |
| gene2tx | Translate gene names to transcript ids using a GTF file for a subset of genes |
| GenomicPlot | GenomicPlot-package |
| get_genomic_feature_coordinates | Extract genomic features from TxDb object |
| get_targeted_genes | Get the number of peaks overlapping each feature of all protein-coding genes |
| get_txdb_features | Get genomic coordinates of features of protein-coding genes |
| gf5_genomic | Toy data for examples and testing of the 'GenomicPlot' package |
| gf5_meta | Toy data for examples and testing of the 'GenomicPlot' package |
| gr2df | Convert GRanges to dataframe |
| handle_bam | Handle files in bam format |
| handle_bed | Handle files in bed|narrowPeak|broadPeak format |
| handle_bedGraph | Handle files in bedGraph format |
| handle_bw | Handle files in bw|bigwig|bigWig|BigWig|BW|BIGWIG format |
| handle_input | Handle import of NGS data with various formats |
| handle_wig | Handle files in wig format |
| input_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package |
| make_subTxDb_from_GTF | Make TxDb object from a GTF file for a subset of genes |
| overlap_pair | Plot two-sets Venn diagram |
| overlap_quad | Plot four-sets Venn diagram |
| overlap_triple | Plot three-sets Venn diagram |
| parallel_countOverlaps | Parallel execution of countOverlaps |
| parallel_scoreMatrixBin | Parallel execution of scoreMatrixBin on a huge target windows object split into chunks |
| plot_5parts_metagene | Plot promoter, 5'UTR, CDS, 3'UTR and TTS |
| plot_bam_correlation | Plot correlation of bam files |
| plot_locus | Plot signal around custom genomic loci |
| plot_locus_with_random | Plot signal around custom genomic loci and random loci for comparison |
| plot_overlap_bed | Plot Venn diagrams depicting overlap of genomic regions |
| plot_overlap_genes | Plot Venn diagrams depicting overlap of gene lists |
| plot_peak_annotation | Annotate peaks with genomic features and genes |
| plot_region | Plot signal inside as well as around custom genomic regions |
| plot_start_end | Plot signals around the start and the end of genomic features |
| plot_start_end_with_random | Plot signals around the start and the end of genomic features and random regions |
| prepare_3parts_genomic_features | Demarcate genes into promoter, gene body and TTS features |
| prepare_5parts_genomic_features | Demarcate genes into promoter, 5'UTR, CDS, 3'UTR and TTS features |
| process_scoreMatrix | Preprocess scoreMatrix before plotting |
| rank_rows | Rank rows of a matrix based on user input |
| rm_outlier | Remove outliers from scoreMatrix |
| setImportParams | set parameters for 'handle_input' function |
| set_seqinfo | Set standard chromosome size of model organisms |
| start_parallel | Prepare for parallel processing |
| stop_parallel | Stop parallel processing |
| test_chip_peak_chr19.bed | Toy data for examples and testing of the 'GenomicPlot' package |
| test_chip_peak_chr19.narrowPeak | Toy data for examples and testing of the 'GenomicPlot' package |
| test_chr19.bedGraph | Toy data for examples and testing of the 'GenomicPlot' package |
| test_clip_peak_chr19.bed | Toy data for examples and testing of the 'GenomicPlot' package |
| test_file1.txt | Toy data for examples and testing of the 'GenomicPlot' package |
| test_file2.txt | Toy data for examples and testing of the 'GenomicPlot' package |
| test_file3.txt | Toy data for examples and testing of the 'GenomicPlot' package |
| test_file4.txt | Toy data for examples and testing of the 'GenomicPlot' package |
| test_wig_chr19_+.bw | Toy data for examples and testing of the 'GenomicPlot' package |
| test_wig_chr19_+.wig | Toy data for examples and testing of the 'GenomicPlot' package |
| treat_chr19.bam | Toy data for examples and testing of the 'GenomicPlot' package |
| txdb.sql | Toy data for examples and testing of the 'GenomicPlot' package |