importFrom(stringr, fixed, str_detect, str_match, str_wrap, str_trunc, str_width)
importFrom(ggplot2, aes, element_text, expansion, geom_point, geom_segment,
           ggplot, ggsave, guide_colorbar, guide_legend, guides, labs,
           scale_color_gradientn, scale_colour_manual,
           scale_size_continuous, scale_x_continuous, scale_y_discrete,
           theme, theme_bw, theme_void, element_rect, waiver, coord_fixed,
           geom_hline, geom_line)
importFrom(ggrepel, geom_label_repel, geom_text_repel)
importFrom(scales, hue_pal, scientific_format, number_format, alpha)
importFrom(dplyr, rename, select, "%>%", arrange, mutate, row_number)
importFrom(tools, file_path_sans_ext)
importFrom(fs, is_absolute_path)
importFrom(rlang, .data)
importFrom(stats, na.omit, weighted.mean, model.matrix, p.adjust, setNames,
           as.formula, complete.cases, coefficients, lm, predict, median,
           prcomp, cor, pf)
importFrom(BiocParallel, bpparam, bplapply)
importFrom(GenomicRanges, GRanges, findOverlaps, reduce, trim, resize, width,
           start, end, seqnames)
importFrom(IRanges, IRanges, ranges)
importFrom(AnnotationHub, AnnotationHub, query, dbconn)
importFrom(ensembldb, genes, metadata)
importFrom(DBI, dbDisconnect)
importFrom(GenomeInfoDb, seqlevels, genome)
importFrom(S4Vectors, queryHits, subjectHits, mcols, "mcols<-")
importFrom(rtracklayer, import)
importFrom(limma, lmFit, makeContrasts, contrasts.fit, eBayes, topTable)
importFrom(NOISeq, noiseq, degenes, readData)
importFrom(BioVenn, draw.venn)
importFrom(tibble, rownames_to_column, column_to_rownames)
importFrom(utils, write.csv, modifyList, head, globalVariables, capture.output, zip, write.table)
importFrom(grDevices, pdf, dev.off, png, rgb)
importFrom(clusterProfiler, bitr, enrichGO, dotplot)
importFrom(enrichplot, dotplot)
importFrom(forcats, fct_reorder)
importFrom(colorspace, darken)
importFrom(ggnewscale, new_scale_colour)
importFrom(methods, is, new, show)
importFrom(DT, datatable, DTOutput, formatRound, renderDT)
importFrom(igvShiny, igvShiny, igvShinyOutput, loadBedGraphTrack, loadBedTrack,
           parseAndValidateGenomeSpec, renderIgvShiny, showGenomicRegion)
importFrom(shiny, fluidPage, h4, hr, mainPanel, observeEvent, p, runApp,
           shinyApp, sidebarLayout, sidebarPanel, titlePanel, actionButton,
           icon, HTML, tags, numericInput)
importFrom(dbscan, kNN, frNN)
importFrom(circlize, colorRamp2)
importFrom(ComplexHeatmap, Heatmap, draw)
importFrom(grid, grid.grabExpr, grid.text, gpar)
importFrom(patchwork, plot_annotation)
importFrom(splines, ns)



export(load_data_peaks)
export(load_data_genes)
export(get_ensdb_genes)
export(reduce_regions)
export(calculate_occupancy)
export(calculate_and_add_occupancy_pvals)
export(filter_genes_by_fdr)
export(differential_binding)
export(differential_accessibility)
export(plot_venn)
export(plot_volcano)
export(quantile_normalisation)
export(quantile_normalization)
export(browse_igv_regions)
export(analyse_go_enrichment)
export(analyze_go_enrichment)
export(sample_labels_by_isolation)
export(extract_unique_sample_ids)
export(analysisTable)
export(conditionNames)
export(enrichedCond1)
export(enrichedCond2)
export(inputData)
export(expressed)
export(plot_limma_diagnostics)
export(plot_input_diagnostics)
