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ChIP-Enrich

R package for gene set enrichment testing using ChIP-seq data.

Description

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.

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Version

Version

1.10.0

License

GPL-3

Maintainer

Chee Lee

Last Published

February 15th, 2017

Functions in chipenrich (1.10.0)

plot_dist_to_tss

Plot histogram of distance from peak to nearest TSS
plot_expected_peaks

Plot the expected number of peaks given locus length for each gene.
supported_methods

List supported methods (enrichment tests)
supported_locusdefs

List supported locus definitions
plot_gene_coverage

Plot gene locus length vs. gene coverage by a peak
plot_spline_length

Plot probability of peak being assigned to a gene vs. gene length
supported_read_lengths

List supported read lengths
supported_genomes

List supported genomes
supported_genesets

List supported genesets
chipenrich

Run ChIP-Enrich on a dataset of ChIP-seq peaks