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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(get_methylation_metric,DGEList)
S3method(get_methylation_metric,data.table)
S3method(get_methylation_metric,default)
S3method(meth_filter,DGEList)
S3method(meth_filter,data.frame)
S3method(meth_filter,data.table)
S3method(prepare_heatmap_data,DGEList)
S3method(prepare_heatmap_data,EList)
S3method(prepare_heatmap_data,default)
S3method(prepare_mds_data,DGEList)
S3method(prepare_mds_data,EList)
S3method(prepare_mds_data,default)
export(annotate_methylation)
export(apply_by_line)
export(catHeader)
export(catHeader_w_tabset)
export(covfile_reader)
export(edgeR_tester)
export(edger_for_rrbs)
export(exponent_format)
export(filter_methylation)
export(find_pvalue_cutoff)
export(fix_nonbreaking_space)
export(genomic_log_trans)
export(get_DE_datatable_updated)
export(get_GO_datatable_updated)
export(get_MD_data_for_all_samples)
export(get_MD_data_for_all_samples_updated)
export(get_MD_data_for_sample)
export(get_delta_methylation)
export(get_enrichment_terms)
export(get_go_terms)
export(get_groupwise_methylation)
export(get_methylation_metric)
export(get_reactome_terms)
export(get_sig_entities_between_conds_across_tissues)
export(get_sig_entities_between_tissues_across_conds)
export(get_sig_entities_from_df)
export(get_sig_entities_from_path)
export(ggplot_MD)
export(ggplot_MD_updated)
export(ggplot_mds)
export(ggplot_mds_repel)
export(ggplot_mds_repel_updated)
export(ggplot_volcano_updated)
export(limorhyde_harmonics)
export(make_venn)
export(merge_cov)
export(meth_filter)
export(minus_log_trans)
export(n_sig_genes_pr_contrast)
export(nearest_timepoint)
export(plot_all_md)
export(plot_density)
export(plot_retained_cpgs)
export(plot_sample_heatmap)
export(plot_top_50_DE_genes_heatmap)
export(prepare_cov_files)
export(prepare_featurecounts)
export(prepare_heatmap_data)
export(prepare_metadata)
export(prepare_rna_dgelist)
export(prepare_rrbs_dgelist)
export(preprocess_methylation_data)
export(print_DE_results)
export(print_DT)
export(print_plotly)
export(remove_shallow_samples)
export(render_markdown_file_single_tissue_updated)
export(replace_na_with_INT)
export(rna_seq_project)
export(run_ontology_tests)
export(scale_this)
export(symlog_trans)
export(volcanoplot)
import(data.table)
import(dplyr)
import(edgeR)
import(forcats)
import(ggplot2)
import(purrr)
import(readr)
import(stringr)
import(tibble)
import(tidyr)
importFrom(data.table,.SD)
importFrom(foreach,"%dopar%")
importFrom(ggplot2,"%+%")