chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

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.

AuthorRyan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut, cre], Laura J. Scott [ths], Maureen A. Sartor [ths]
Date of publicationNone
MaintainerRaymond G. Cavalcante <rcavalca@umich.edu>
LicenseGPL-3
Version1.12.0

View on Bioconductor

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

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