Files in chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

R/peaks_per_gene.R R/peak_weights.R R/broadenrich.R R/test_chipenrich.R R/test_approx.R R/polyenrich.R R/test_polyapprox.R R/test_polyenrich_weighted.R R/test_binomial.R R/utils.R R/hybrid.R R/assign_peaks.R R/test_broadenrich.R R/peaks2genes.R R/test_chipenrich_slow.R R/chipenrich.R R/randomize.R R/test_proxReg.R R/proxReg.R R/read.R R/plot_chipenrich_spline.R R/plot_gene_coverage.R R/supported.R R/plot_polyenrich_spline.R R/test_polyenrich.R R/setup.R R/chipenrich_package_doc.R R/test_chipapprox.R R/plot_dist_to_tss.R R/constants.R R/test_polyenrich_slow.R R/test_fisher.R vignettes/chipenrich-vignette.Rmd man/read_geneset.Rd man/load_peaks.Rd man/setup_locusdef.Rd man/read_mappa.Rd man/read_bed.Rd man/peaks2genes.Rd man/supported_genesets.Rd man/read_ldef.Rd man/plot_gene_coverage.Rd man/supported_locusdefs.Rd man/supported_read_lengths.Rd man/genome_to_orgdb.Rd man/plot_dist_to_tss.Rd man/supported_methods.Rd man/get_test_method.Rd man/chipenrich_package.Rd man/broadenrich.Rd man/postprocess_peak_grs.Rd man/proxReg.Rd man/setup_mappa.Rd man/plot_chipenrich_spline.Rd man/post_process_enrichments.Rd man/chipenrich.Rd man/calc_peak_gene_overlap.Rd man/num_peaks_per_gene.Rd man/polyenrich.Rd man/plot_polyenrich_spline.Rd man/supported_genomes.Rd man/reset_ncores_for_windows.Rd man/assign_peak_segments.Rd man/genome_to_organism.Rd man/setup_genesets.Rd man/filter_genesets.Rd man/recode_peaks.Rd man/hybridenrich.Rd man/assign_peaks.Rd tests/testthat.R tests/testthat/test_0c_supported.R tests/testthat/test_0b_setup.R tests/testthat/test_3_peaks_per_gene.R tests/testthat/test_1_read.R tests/testthat/test_4_randomize.R tests/testthat/test_0a_utils.R tests/testthat/test_5_chipenrich.R tests/testthat/test_6_qcplots.R tests/testthat/test_2_assign_peaks.R

inst/CITATION

inst/doc/chipenrich-vignette.html

inst/doc/chipenrich-vignette.R inst/doc/chipenrich-vignette.Rmd

inst/extdata/test.broadPeak

inst/extdata/test_mappa_one.txt

inst/extdata/test.bedGraph

inst/extdata/test_ldef_noextras.txt

inst/extdata/test.broadPeak.gz

inst/extdata/test_noheader.txt

inst/extdata/test_ldef_symbol.txt

inst/extdata/test_mappa_badhead.txt

inst/extdata/test.narrowPeak.gz

inst/extdata/test_ldef_nosymbol.txt

inst/extdata/test_geneset.txt

inst/extdata/test.narrowPeak

inst/extdata/test.gff3

inst/extdata/test_ldef_geneid.txt

inst/extdata/vignette_genesets.txt

inst/extdata/test_assign.bed

inst/extdata/test_header.txt

inst/extdata/test_header.bed

inst/extdata/test_mappa_dup.txt

inst/extdata/test.gff3.gz

inst/extdata/test_mappa_good.txt

inst/extdata/test_mappa_neg.txt

inst/extdata/test_ppg.txt

chipenrich documentation built on Nov. 8, 2020, 8:11 p.m.