chipenrich-package | Run ChIP-Enrich on a dataset of ChIP-seq peaks |
assign_peaks | Assign peak midpoints to defined gene loci. |
assign_peak_segments | Assign whole peaks to all overlapping defined gene loci. |
calc_peak_gene_overlap | Add peak overlap and ratio to result of 'num_peaks_per_gene()' |
chipenrich | Run ChIP-Enrich on a dataset of ChIP-seq peaks |
load_peaks | Convert BEDX+Y data.frames and into GRanges |
num_peaks_per_gene | Aggregate peak assignments over the 'geneid' column |
plot_dist_to_tss | Plot histogram of distance from peak to nearest TSS |
plot_gene_coverage | Plot probability of peak being assigned to a gene vs. gene length |
plot_spline_length | Plot probability of peak being assigned to a gene vs. gene length |
read_bed | Read BEDX+Y files and convert into GRanges |
read_bedgff | Read BEDGFF files and convert into GRanges |
supported_genesets | Display supported genesets for gene set enrichment. |
supported_genomes | Display supported genomes. |
supported_locusdefs | Display supported locus definitions |
supported_methods | Display supported gene set enrichment methods. |
supported_read_lengths | Display supported read lengths for mappability |