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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("%>%")
export(G_correction)
export(ShiftScores)
export(annotate_features)
export(apply_threshold)
export(associate_with_tsr)
export(conditionals)
export(differential_expression)
export(export_for_enrichment)
export(extract_counts)
export(extract_de)
export(extract_matrix)
export(fit_de_model)
export(format_counts)
export(gene_tracks)
export(get_annotation)
export(get_assembly)
export(get_counts)
export(get_diff_model)
export(get_diff_results)
export(get_granges)
export(get_sample_sheet)
export(get_shifting_results)
export(import_bams)
export(mark_dominant)
export(merge_samples)
export(normalize_counts)
export(ordering)
export(plot_correlation)
export(plot_density)
export(plot_detected_features)
export(plot_dinucleotide_frequencies)
export(plot_genomic_distribution)
export(plot_heatmap)
export(plot_ma)
export(plot_num_de)
export(plot_reduction)
export(plot_sequence_colormap)
export(plot_sequence_logo)
export(plot_shift_count)
export(plot_shift_rank)
export(plot_threshold_exploration)
export(plot_tsr_metric)
export(plot_volcano)
export(quantiling)
export(retrieve_seqs)
export(set_count_slot)
export(softclip_composition)
export(softclip_histogram)
export(tsr_experiment)
export(tsr_explorer)
export(tsr_export)
export(tsr_import)
export(tsr_metrics)
export(tss_aggregate)
export(tss_clustering)
export(tss_experiment)
export(tss_export)
export(tss_import)
export(tss_shift)
exportClasses(tsr_explorer)
import(data.table)
import(methods)
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,width)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,consensusMatrix)
importFrom(Biostrings,getSeq)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,isCircular)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,makeTxDbFromGFF)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicFeatures,transcripts)
importFrom(GenomicRanges,GRanges)
importFrom(Rcpp,sourceCpp)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(assertthat,assert_that)
importFrom(assertthat,has_attr)
importFrom(assertthat,has_name)
importFrom(assertthat,is.count)
importFrom(assertthat,is.flag)
importFrom(assertthat,is.readable)
importFrom(assertthat,is.string)
importFrom(circlize,colorRamp2)
importFrom(dplyr,bind_cols)
importFrom(dplyr,case_when)
importFrom(dplyr,dense_rank)
importFrom(dplyr,desc)
importFrom(dplyr,ntile)
importFrom(dplyr,pull)
importFrom(forcats,fct_inorder)
importFrom(forcats,fct_recode)
importFrom(forcats,fct_relevel)
importFrom(forcats,fct_reorder)
importFrom(forcats,fct_rev)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_continuous)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_color_viridis_c)
importFrom(ggplot2,scale_color_viridis_d)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_fill_viridis_c)
importFrom(ggplot2,scale_fill_viridis_d)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(grid,gpar)
importFrom(grid,grid.text)
importFrom(magrittr,"%>%")
importFrom(plyranges,anchor_3p)
importFrom(plyranges,anchor_5p)
importFrom(plyranges,anchor_center)
importFrom(plyranges,as_granges)
importFrom(plyranges,bind_ranges)
importFrom(plyranges,join_overlap_left_directed)
importFrom(plyranges,mutate)
importFrom(plyranges,reduce_ranges_directed)
importFrom(plyranges,stretch)
importFrom(purrr,discard)
importFrom(purrr,flatten)
importFrom(purrr,imap)
importFrom(purrr,iwalk)
importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,map_df)
importFrom(purrr,map_lgl)
importFrom(purrr,pmap)
importFrom(purrr,walk)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,.data)
importFrom(rlang,enquo)
importFrom(rlang,enquos)
importFrom(rlang,ensym)
importFrom(rlang,quo_is_null)
importFrom(rlang,quo_text)
importFrom(rtracklayer,export)
importFrom(rtracklayer,import)
importFrom(stats,as.formula)
importFrom(stats,cor)
importFrom(stats,ecdf)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,rbinom)
importFrom(stringr,str_c)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_length)
importFrom(stringr,str_pad)
importFrom(stringr,str_replace)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_to_lower)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,replace_na)
importFrom(viridis,viridis)
useDynLib(TSRexploreR, .registration=TRUE)