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NAMESPACE
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84 lines (83 loc) · 2.28 KB
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# Generated by roxygen2: do not edit by hand
S3method(print,DoseRider)
export(DoseRider)
export(DoseRiderParallel)
export(add_best_model_adj_pvalue)
export(as.data.frame.DoseRider)
export(compute_IC50)
export(compute_bmd_bounds_parallel)
export(compute_bmd_bounds_sequential)
export(compute_bmd_for_gene_in_geneset)
export(compute_bmd_from_main_trend)
export(compute_derivatives)
export(create_gene_heatmap)
export(create_lmm_formula)
export(create_summarized_experiment)
export(dose_response_heatmap)
export(estimate_model_parameters)
export(extract_bmd_for_pathway)
export(extract_tcd_for_pathway)
export(filter_DoseRider)
export(filter_gmt_by_size)
export(find_geneset_index)
export(get_bmd_range)
export(get_tcd_range)
export(loadCPDB)
export(plot_bmd_confidence_intervals)
export(plot_bmd_density_and_peaks)
export(plot_dotplot_top_pathways)
export(plot_gene_random_effect_relationship)
export(plot_gene_set_random_effects)
export(plot_pathway_response)
export(plot_tcd1_confidence_intervals)
export(plot_tcd_density)
export(plot_top_pathway_responses)
export(prepare_data)
export(process_gene_set)
export(read_gmt)
import(SummarizedExperiment)
import(doParallel)
import(dplyr)
import(drc)
import(foreach)
import(ggplot2)
import(ggrepel)
import(ggridges)
import(parallel)
import(progress)
import(tidyr)
import(utils)
importFrom(AICcmodavg,AICc)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(MASS,negative.binomial)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(circlize,colorRamp2)
importFrom(cluster,silhouette)
importFrom(cowplot,plot_grid)
importFrom(doSNOW,registerDoSNOW)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,estimateDisp)
importFrom(factoextra,fviz_nbclust)
importFrom(gammit,extract_ranef)
importFrom(grid,gpar)
importFrom(lme4,glmer)
importFrom(lme4,glmerControl)
importFrom(lme4,lmer)
importFrom(lme4,ranef)
importFrom(mgcv,anova.gam)
importFrom(mgcv,bam)
importFrom(performance,icc)
importFrom(reshape,melt)
importFrom(reshape2,dcast)
importFrom(splines,bs)
importFrom(stats,formula)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,predict)
importFrom(stringr,str_replace)
importFrom(stringr,str_wrap)
importFrom(tidyr,spread)
importFrom(utils,globalVariables)
importFrom(utils,txtProgressBar)