| annotate_chip | Annotate "chip.data", given as parameter. |
| annotate_region | Annotates a set of regions with genomic features. |
| annotate_venn_center | Annotate the inner group of an 'intersect.object'. |
| annotate_venn_exclusive | Annotate the outer groups of an 'intersect.object'. |
| associate_chrom_state | Associate chromatin sates to a GRanges object. |
| associate_fitness_genes | Identify essential genes of a GRanges object. |
| associate_gene_chip | Associate genes to a GRanges object from ChIP-seq data. |
| associate_genomic_region | Associate genomic regions to a GRanges object. |
| associate_histone_marks | Associate histone marks to a GRanges object. |
| associate_is_gene_active | Associates a boolean in fonction of the activity of the gene |
| associate_tf | Associate TF overlaps to a GRanges object. |
| associate_tissue_specificity_human | Associate tissue specificity of genes to a GRanges object. |
| build_intersect | Given a GRangesList object, determine which items overlap... |
| build_intersect_all | Builds an overlap of the given regions and output all default... |
| characterize_gene_set | Given a set of Entrez gene ids, perform KEGG enrichment and... |
| characterize_region | Given a set of regions, perform annotation, motif enrichment... |
| chrom_state_match | Given a set of regions and a chromatin state map, match the... |
| collapse_regions | Collapses a list of genomic ranges into a single set of... |
| csaw_analyze | Analyze bam files with csaw and produces corresponding... |
| csaw.save.plots | Output of csaw analysis |
| default_download_filter_chip | Default filtering function for 'download_encode_chip'. |
| default_download_filter_rna | Default filtering function for 'download_encode_rna'. |
| download_chromatin_states | Helper function for obtaining chromatin states through... |
| download_encode_chip | Obtains and process transcription factor data from ENCODE. |
| download_encode_histones | Helper function for obtaining histone data through... |
| download_encode_polymerases | Helper function for obtaining polymerase data through... |
| download_encode_rna | Obtains and process expression data from ENCODE. |
| download_encode_tf | Helper function for obtaining transcription factor data... |
| download.one.chrom.state | Download a single chromatin state map from ENCODE. |
| exclusive.overlap.internal | Internal exclusive overlap. |
| filter.reads.to.counts | Filter out unintersing windows, by global enrichment method. |
| gene_from_regions | Given a set of regions, convert it to a set of Entrez gene... |
| gene_peaks_distances | Generate a summary of the distances separating a set of genes... |
| get.chrom.state.url | Given a mnemonic and a number of states, builds the download... |
| get_encode_mnemonic | Given a biosample's name, tries to match it with an ENCODE... |
| get_promoters | Given a set of Entrez IDS, retrieve the coordinates of those... |
| histone_download_filter_chip | Alternative filtering function for 'download_encode_chip'. |
| import.and.discard.metadata | Import a bed file and discards its metadata. |
| import_chrom_states | Import HMM chromatin states for the right cell type. |
| import_files_into_grl | Import a set of bed-lie files into a GRangesList. |
| import_into_grl | Import a set of bed files in a directory into a GRangesList. |
| inclusive.overlap.internal | Internal inclusive overlap. |
| install_annotations | Install required annotation packages. |
| intersect_overlap | Calculate an overlap of certain factors within an... |
| intersect_venn_plot | Generates a venn diagram from an 'intersect.object'. |
| isoform_download_filter_rna | Alternative filtering function for 'download_encode_rna'. |
| kegg_enrichment | Perform KEGG pathway enrichment on a set of genes. |
| kegg_enrichment_regions | Perform KEGG enrichment on a set of regions. |
| load_chrom_state | Given the name of a bed file containing a chromatin state... |
| motif_enrichment | Given a GRanges object, finds enriched motifs within those... |
| motif_enrichment_genes | Perform motif enrichment on the promoters of a set of genes. |
| multiple_keggs_plot | Generates a plot representing significant kegg pathways from... |
| multiple_region_enrichment | Performs region enrichment on a set of regions and returns... |
| multiple.testing | Make corrections for multiple testing |
| normalization.factors | Calculate normalization factors, by using TMM method. |
| pairwise_overlap | Calculate the pairwise overlaps of all factors within an... |
| partition_genomic_regions | Generate a GRanges object partitioning the genome into... |
| pol2_download_filter_chip | Alternative filtering function for 'download_encode_chip'. |
| post_processing | Save results of 'multiple.testing' with annotations |
| project_ranges | Projects the ranges in query into the ranges in target. |
| read_identical | Import a set of identically structured files. |
| reads.to.counts | Convert reads from bam files to counts |
| region_consensus | Obtains consensus regions from a set of regions. |
| region_enrichment | Calculates enrichment ratios for quer regions against a... |
| region_enrichment_summary | Performs a summary of region enrichment results. |
| region_overlap | Generate a matrix detailing the percentage of overlap between... |
| select_annotations | Annotations selection helper. |
| simple_chrom_state_map | Returns the mapping used to go from full chromatin states to... |
| simplify_chrom_state | Simplifies chromatin state names. |
| test.diff.binding | Test the differential binding. |
