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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(annotate_chip)
export(annotate_region)
export(annotate_venn_center)
export(annotate_venn_exclusive)
export(associate_chrom_state)
export(associate_fitness_genes)
export(associate_gene_chip)
export(associate_genomic_region)
export(associate_histone_marks)
export(associate_is_gene_active)
export(associate_tf)
export(associate_tissue_specificity_human)
export(build_intersect)
export(build_intersect_all)
export(characterize_gene_set)
export(characterize_region)
export(chrom_state_match)
export(collapse_regions)
export(csaw_analyze)
export(default_download_filter_chip)
export(default_download_filter_rna)
export(do.GO.enrichment)
export(download_chromatin_states)
export(download_encode_chip)
export(download_encode_histones)
export(download_encode_polymerases)
export(download_encode_rna)
export(download_encode_tf)
export(gene_from_regions)
export(gene_peaks_distances)
export(get_encode_mnemonic)
export(get_promoters)
export(histone_download_filter_chip)
export(import_chrom_states)
export(import_files_into_grl)
export(import_into_grl)
export(install_annotations)
export(intersect_overlap)
export(intersect_venn_plot)
export(isoform_download_filter_rna)
export(kegg_enrichment)
export(kegg_enrichment_regions)
export(load_chrom_state)
export(motif_enrichment)
export(motif_enrichment_genes)
export(multiple_keggs_plot)
export(multiple_region_enrichment)
export(pairwise_overlap)
export(partition_genomic_regions)
export(pol2_download_filter_chip)
export(post_processing)
export(project_ranges)
export(read_identical)
export(region_consensus)
export(region_enrichment)
export(region_enrichment_summary)
export(region_overlap)
export(select_annotations)
export(simple_chrom_state_map)
export(simplify_chrom_state)
import(GenomicRanges)
import(csaw)
import(edgeR)
import(ggplot2)
import(topGO)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,select)
importFrom(Biobase,cache)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,getSeq)
importFrom(ChIPseeker,annotatePeak)
importFrom(ENCODExplorer,downloadEncode)
importFrom(ENCODExplorer,queryEncode)
importFrom(GenomicFeatures,exonsBy)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,transcriptsBy)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,reduce)
importFrom(PWMEnrich,groupReport)
importFrom(PWMEnrich,motifEnrichment)
importFrom(PWMEnrich,plotMultipleMotifs)
importFrom(VennDiagram,venn.diagram)
importFrom(csaw,asDGEList)
importFrom(csaw,filterWindows)
importFrom(csaw,normOffsets)
importFrom(csaw,windowCounts)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,plot)
importFrom(plyr,ddply)
importFrom(plyr,mutate)
importFrom(reshape2,melt)
importFrom(rtracklayer,import)
importFrom(stats,aggregate)
importFrom(stats,model.matrix)
importFrom(stats,relevel)
importFrom(utils,download.file)
importFrom(utils,write.table)
importMethodsFrom(BSgenome,width)
importMethodsFrom(GenomicRanges,countOverlaps)
importMethodsFrom(GenomicRanges,findOverlaps)
importMethodsFrom(GenomicRanges,range)
importMethodsFrom(GenomicRanges,ranges)
importMethodsFrom(GenomicRanges,reduce)