Man pages for jokergoo/cotools
R functions
| add_subtype_specificity | ad subtype specificity columns |
| annotate_to_gene_models | Annotate to gene models |
| annotate_to_genomic_features | simple annotation to genomic features |
| available_gencode_field | Returns all supported fields in gtf data |
| basic_genomic_regions_stat | Basic statistics on genomic regions |
| bp | define bp |
| chromatin_states_transition_chord_diagram | chord diagram for chromatin states transistion |
| common_regions | Find common genomic regions across several samples |
| compare_meth | compare methylation between smoothed and raw methylation data |
| correlated_regions | correlated regions |
| correlated_regions_per_gene | correlated regions in extended gene model |
| cr_enriched_at_tss | enrichment of cr on tss |
| cr_gviz | Customized Gviz plot for a gene model |
| cr_hilbert | Hilbert curve visualization of CRs |
| cr_overlap_to_genomic_features | enrichment between cr and genomic feature |
| cr_qc | QC on crs |
| cr_scatterplot_me | Scatter plot between methylation and expression |
| enriched_heatmap_list_on_gene | Enriched heatmap |
| enriched_heatmap_list_on_genomic_features | Enriched heatmap on a certain gf |
| enriched_heatmap_list_on_tss_cgi | Enriched heatmap on TSS-CGI |
| extract_field_from_gencode | Extract field from gencode GTF file |
| extract_sites | Extract subset of sites which are in a set of intervals |
| filter_correlated_regions | filter correlation regions |
| genomicCorr.absdist | Absolute distance between two sets of genomic regions |
| genomicCorr.jaccard | Jaccard coefficient between two sets of genomic regions |
| genomicCorr.nintersect | Intersections between two sets of genomic regions |
| genomicCorr.pintersect | Intersection between two sets of genomic regions |
| genomicCorr.reldist | Relative distance between two sets of genomic regions |
| genomicCorr.sintersect | Intersection between two sets of genomic regions |
| genomic_regions_correlation | Correlation between two sets of genomic regions |
| get_mean_methylation_in_genomic_features | Calculate mean methylation value in a list of regions |
| global_methylation_distribution | Global methylation distribution |
| heatmap_diff_methylation_in_genomic_features | Heatmap for mean methylation in genomic features |
| kb | define kb |
| logical_segment | segment by continuous logical values |
| mb | define mb |
| methylation_hooks | Hook functions to extract methylation |
| percentOverlaps | For every interval in 'query', percent that is covered by... |
| plot_coverage_and_methylation_on_genome | coverage and methylation for one sample |
| plot_multiple_samples_methylation_on_genome | methylation for more than one samples |
| plot_subgroup_specificity_heatmap | heatmap for visualizing subgroup specific genomic regions |
| print.bp | print bp class objects |
| reduce2 | reduce based on the width of the interval |
| reduce_cr | refuce cr regions |
| reduce_cr_gap_test | plot that helps to choose a gap |
| scatterplot_with_boxplot | scatterplot with boxplots on both sides |
| subgroup_specific_genomic_regions | find subgroup specific regions |
| systemdf | Wrapper of system calls in which input and output are all... |
| wgbs_qcplot | Basic qc plot for bisulfite sequencing data |
