# Generated by roxygen2: do not edit by hand

S3method(extract_rectangle,character)
S3method(extract_rectangle,data.table)
S3method(extract_rectangle,matrix)
S3method(guess_maxquant_quantity,SummarizedExperiment)
S3method(guess_maxquant_quantity,character)
S3method(guess_maxquant_quantity,data.frame)
S3method(guess_sep,SummarizedExperiment)
S3method(guess_sep,character)
S3method(guess_sep,factor)
S3method(invert,SummarizedExperiment)
S3method(invert,character)
S3method(standardize_maxquant_snames,SummarizedExperiment)
S3method(standardize_maxquant_snames,character)
export("analysis<-")
export("contrastdefs<-")
export("counts<-")
export("cpm<-")
export("fdata<-")
export("fnames<-")
export("fvars<-")
export("is_imputed<-")
export("limma<-")
export("log2counts<-")
export("log2countsratios<-")
export("log2cpm<-")
export("log2cpmratios<-")
export("log2tpm<-")
export("log2tpmratios<-")
export("occupancies<-")
export("proteingroups<-")
export("sdata<-")
export("snames<-")
export("svalues<-")
export("svars<-")
export("tpm<-")
export("values<-")
export("weights<-")
export(.read_maxquant)
export(.read_metabolon)
export(.read_rectangles)
export(.read_rnaseq_bams)
export(.read_rnaseq_counts)
export(.read_somascan)
export(AUTONOMICS_DATASETS)
export(MAXQUANT_PATTERNS_PEPCOUNTS)
export(MAXQUANT_PATTERNS_QUANTITY)
export(TESTS)
export(add_smiles)
export(analysis)
export(analyze)
export(assert_is_valid_sumexp)
export(biplot)
export(biplot_corrections)
export(biplot_covariates)
export(center)
export(contrast_subgroup_cols)
export(contrast_subgroup_rows)
export(contrastdefs)
export(counts)
export(counts2cpm)
export(counts2tpm)
export(cpm)
export(cpm2counts)
export(create_design)
export(create_sfile)
export(default_formula)
export(default_sfile)
export(default_subgroupvar)
export(download_data)
export(download_gtf)
export(dt2mat)
export(exp2)
export(explore_imputations)
export(explore_transformations)
export(extract_features)
export(extract_rectangle)
export(fdata)
export(filter_exprs_replicated_in_some_subgroup)
export(filter_features)
export(filter_medoid)
export(filter_replicated)
export(filter_samples)
export(fit_limma)
export(fit_lm)
export(fit_lme)
export(fit_lmer)
export(fit_wilcoxon)
export(flevels)
export(fnames)
export(formula2str)
export(fvalues)
export(fvars)
export(guess_maxquant_quantity)
export(guess_sep)
export(halfnormimpute)
export(impute_systematic_nondetects)
export(inf_to_na)
export(invert)
export(invnorm)
export(is_imputed)
export(is_sig)
export(lda)
export(limma)
export(log2counts)
export(log2countsratios)
export(log2cpm)
export(log2cpmratios)
export(log2tpm)
export(log2tpmratios)
export(log2transform)
export(make_volcano_dt)
export(mat2dt)
export(matrix2sumexp)
export(merge_fdata)
export(merge_ffile)
export(merge_sdata)
export(merge_sfile)
export(message_df)
export(minusinf_to_na)
export(na_to_zero)
export(nan_to_na)
export(nfactors)
export(normimpute)
export(occupancies)
export(pca)
export(plot_biplot)
export(plot_boxplots)
export(plot_contrastogram)
export(plot_corrections)
export(plot_covariates)
export(plot_data)
export(plot_densities)
export(plot_detections)
export(plot_detects)
export(plot_feature_boxplots)
export(plot_feature_densities)
export(plot_feature_profiles)
export(plot_feature_violins)
export(plot_features)
export(plot_quantifications)
export(plot_sample_boxplots)
export(plot_sample_densities)
export(plot_sample_violins)
export(plot_subgroup_boxplots)
export(plot_subgroup_violins)
export(plot_summarized_detections)
export(plot_venn)
export(plot_violins)
export(plot_volcano)
export(pls)
export(preprocess_rnaseq_counts)
export(proteingroups)
export(quantnorm)
export(read_affymetrix)
export(read_metabolon)
export(read_phosphosites)
export(read_proteingroups)
export(read_rectangles)
export(read_rnaseq_bams)
export(read_rnaseq_counts)
export(read_somascan)
export(rm_singleton_samples)
export(sampleid_values)
export(scaledlibsizes)
export(sdata)
export(slevels)
export(sma)
export(snames)
export(split_by_svar)
export(split_extract)
export(standardize_maxquant_snames)
export(subgroup_array)
export(subgroup_levels)
export(subgroup_matrix)
export(subgroup_values)
export(subtract_baseline)
export(subtract_differences)
export(subtract_pairs)
export(sumexp2mae)
export(sumexp_to_long_dt)
export(sumexp_to_subrep_dt)
export(sumexp_to_wide_dt)
export(summarize_fit)
export(svalues)
export(svars)
export(tpm)
export(translate)
export(values)
export(venn_detects)
export(weights)
export(zero_to_na)
export(zeroimpute)
export(zscore)
exportMethods(analysis)
import(ggplot2)
import(stringi)
importFrom(BiocGenerics,cbind)
importFrom(MultiAssayExperiment,"colData<-")
importFrom(MultiAssayExperiment,"experiments<-")
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,colData)
importFrom(MultiAssayExperiment,experiments)
importFrom(R.utils,gunzip)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,makeSummarizedExperimentFromExpressionSet)
importFrom(SummarizedExperiment,rowData)
importFrom(abind,adrop)
importFrom(assertive,assert_all_are_dirs)
importFrom(assertive,assert_all_are_existing_files)
importFrom(assertive,assert_all_are_finite)
importFrom(assertive,assert_all_are_greater_than)
importFrom(assertive,assert_all_are_in_closed_range)
importFrom(assertive,assert_all_are_in_range)
importFrom(assertive,assert_all_are_less_than_or_equal_to)
importFrom(assertive,assert_all_are_non_missing_nor_empty_character)
importFrom(assertive,assert_all_are_not_matching_fixed)
importFrom(assertive,assert_all_are_true)
importFrom(assertive,assert_all_are_whole_numbers)
importFrom(assertive,assert_any_are_not_nan)
importFrom(assertive,assert_any_are_true)
importFrom(assertive,assert_are_identical)
importFrom(assertive,assert_are_same_length)
importFrom(assertive,assert_engine)
importFrom(assertive,assert_has_names)
importFrom(assertive,assert_has_no_duplicates)
importFrom(assertive,assert_is_a_bool)
importFrom(assertive,assert_is_a_number)
importFrom(assertive,assert_is_a_string)
importFrom(assertive,assert_is_all_of)
importFrom(assertive,assert_is_any_of)
importFrom(assertive,assert_is_character)
importFrom(assertive,assert_is_data.frame)
importFrom(assertive,assert_is_function)
importFrom(assertive,assert_is_identical_to_true)
importFrom(assertive,assert_is_list)
importFrom(assertive,assert_is_logical)
importFrom(assertive,assert_is_matrix)
importFrom(assertive,assert_is_non_empty)
importFrom(assertive,assert_is_non_scalar)
importFrom(assertive,assert_is_not_null)
importFrom(assertive,assert_is_numeric)
importFrom(assertive,assert_is_of_length)
importFrom(assertive,assert_is_subset)
importFrom(assertive,false)
importFrom(assertive,get_name_in_parent)
importFrom(assertive,has_names)
importFrom(assertive,has_no_duplicates)
importFrom(assertive,is_a_string)
importFrom(assertive,is_empty_character)
importFrom(assertive,is_existing_file)
importFrom(assertive,is_formula)
importFrom(assertive,is_scalar)
importFrom(assertive,is_subset)
importFrom(colorspace,sequential_hcl)
importFrom(data.table,":=")
importFrom(data.table,.I)
importFrom(data.table,.N)
importFrom(data.table,.SD)
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,dcast.data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,is.data.table)
importFrom(data.table,melt.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(data.table,setorderv)
importFrom(data.table,tstrsplit)
importFrom(edgeR,filterByExpr)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,hcl)
importFrom(graphics,layout)
importFrom(graphics,lines)
importFrom(graphics,pie)
importFrom(graphics,title)
importFrom(grid,grid.draw)
importFrom(grid,grid.layout)
importFrom(grid,grid.newpage)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(limma,contrasts.fit)
importFrom(limma,duplicateCorrelation)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,removeBatchEffect)
importFrom(limma,vennDiagram)
importFrom(limma,voom)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(magrittr,add)
importFrom(magrittr,and)
importFrom(magrittr,divide_by)
importFrom(magrittr,equals)
importFrom(magrittr,extract)
importFrom(magrittr,extract2)
importFrom(magrittr,is_in)
importFrom(magrittr,multiply_by)
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_names)
importFrom(magrittr,set_rownames)
importFrom(magrittr,subtract)
importFrom(matrixStats,colAnys)
importFrom(matrixStats,colWeightedMeans)
importFrom(matrixStats,rowAlls)
importFrom(matrixStats,rowAnys)
importFrom(matrixStats,rowSds)
importFrom(methods,as)
importFrom(methods,is)
importFrom(parallel,detectCores)
importFrom(readxl,excel_sheets)
importFrom(readxl,read_excel)
importFrom(rlang,as_name)
importFrom(rlang,as_string)
importFrom(rlang,enexpr)
importFrom(rlang,enquo)
importFrom(rlang,eval_tidy)
importFrom(rlang,expr_text)
importFrom(rlang,quo_is_null)
importFrom(rlang,quo_name)
importFrom(stats,aggregate)
importFrom(stats,approxfun)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,lowess)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.exclude)
importFrom(stats,p.adjust)
importFrom(stats,qnorm)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,wilcox.test)
importFrom(tidyr,separate_rows)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(utils,adist)
importFrom(utils,capture.output)
importFrom(utils,count.fields)
importFrom(utils,download.file)
importFrom(utils,getFromNamespace)
importFrom(utils,installed.packages)
importFrom(utils,unzip)
