chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Share:

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 <rcavalca@umich.edu>
License
GPL-3
Version
1.12.0

View on Bioconductor

Man pages

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

Files in this package

chipenrich/DESCRIPTION
chipenrich/NAMESPACE
chipenrich/NEWS
chipenrich/R
chipenrich/R/assign_peaks.R
chipenrich/R/chipenrich.R
chipenrich/R/chipenrich_package_doc.R
chipenrich/R/constants.R
chipenrich/R/peaks_per_gene.R
chipenrich/R/plot_dist_to_tss.R
chipenrich/R/plot_gene_coverage.R
chipenrich/R/plot_spline_length.R
chipenrich/R/randomize.R
chipenrich/R/read.R
chipenrich/R/setup.R
chipenrich/R/supported.R
chipenrich/R/test_approx.R
chipenrich/R/test_binomial.R
chipenrich/R/test_fisher.R
chipenrich/R/test_gam.R
chipenrich/R/utils.R
chipenrich/README.md
chipenrich/build
chipenrich/build/vignette.rds
chipenrich/inst
chipenrich/inst/CITATION
chipenrich/inst/doc
chipenrich/inst/doc/chipenrich-vignette.R
chipenrich/inst/doc/chipenrich-vignette.Rmd
chipenrich/inst/doc/chipenrich-vignette.html
chipenrich/inst/extdata
chipenrich/inst/extdata/test.broadPeak
chipenrich/inst/extdata/test.broadPeak.gz
chipenrich/inst/extdata/test.gff3
chipenrich/inst/extdata/test.gff3.gz
chipenrich/inst/extdata/test.narrowPeak
chipenrich/inst/extdata/test.narrowPeak.gz
chipenrich/inst/extdata/test_assign.bed
chipenrich/inst/extdata/test_geneset.txt
chipenrich/inst/extdata/test_header.bed
chipenrich/inst/extdata/vignette_genesets.txt
chipenrich/man
chipenrich/man/assign_peak_segments.Rd
chipenrich/man/assign_peaks.Rd
chipenrich/man/calc_peak_gene_overlap.Rd
chipenrich/man/chipenrich.Rd
chipenrich/man/load_peaks.Rd
chipenrich/man/num_peaks_per_gene.Rd
chipenrich/man/plot_dist_to_tss.Rd
chipenrich/man/plot_gene_coverage.Rd
chipenrich/man/plot_spline_length.Rd
chipenrich/man/read_bed.Rd
chipenrich/man/read_bedgff.Rd
chipenrich/man/supported_genesets.Rd
chipenrich/man/supported_genomes.Rd
chipenrich/man/supported_locusdefs.Rd
chipenrich/man/supported_methods.Rd
chipenrich/man/supported_read_lengths.Rd
chipenrich/tests
chipenrich/tests/testthat
chipenrich/tests/testthat.R
chipenrich/tests/testthat/test_assign_peaks.R
chipenrich/tests/testthat/test_peak_input.R
chipenrich/tests/testthat/test_peaks_per_gene.R
chipenrich/tests/testthat/test_user_geneset.R
chipenrich/vignettes
chipenrich/vignettes/chipenrich-vignette.Rmd