ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.
|Author||Ryan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths]|
|Date of publication||None|
|Maintainer||Raymond G. Cavalcante <firstname.lastname@example.org>|
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...
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...
plot_spline_length: Plot probability of peak being assigned to a gene vs. gene...
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