# Generated by roxygen2: do not edit by hand

S3method(arrange,tidybulk)
S3method(bind_cols,tidybulk)
S3method(bind_rows,tidybulk)
S3method(distinct,tidybulk)
S3method(filter,tidybulk)
S3method(full_join,tidybulk)
S3method(group_by,tidybulk)
S3method(inner_join,tidybulk)
S3method(left_join,tidybulk)
S3method(mutate,nested_tidybulk)
S3method(mutate,tidybulk)
S3method(nest,tidybulk)
S3method(rename,tidybulk)
S3method(right_join,tidybulk)
S3method(rowwise,tidybulk)
S3method(summarise,tidybulk)
S3method(ungroup,tidybulk)
S3method(unnest,nested_tidybulk)
export("%>%")
export(adjust_abundance)
export(aggregate_duplicates)
export(arrange)
export(as_SummarizedExperiment)
export(as_matrix)
export(as_tibble)
export(bind_cols)
export(cluster_elements)
export(deconvolve_cellularity)
export(describe_transcript)
export(distinct)
export(do)
export(ensembl_to_symbol)
export(fill_missing_abundance)
export(filter)
export(full_join)
export(get_bibliography)
export(group_by)
export(identify_abundant)
export(impute_missing_abundance)
export(inner_join)
export(keep_abundant)
export(keep_variable)
export(left_join)
export(log10_reverse_trans)
export(logit_trans)
export(mutate)
export(nest)
export(pivot_sample)
export(pivot_transcript)
export(quantile_normalise_abundance)
export(reduce_dimensions)
export(remove_redundancy)
export(rename)
export(resolve_complete_confounders_of_non_interest)
export(right_join)
export(rotate_dimensions)
export(rowwise)
export(scale_abundance)
export(select)
export(summarise)
export(symbol_to_entrez)
export(test_differential_abundance)
export(test_differential_cellularity)
export(test_gene_enrichment)
export(test_gene_overrepresentation)
export(test_gene_rank)
export(test_stratification_cellularity)
export(tibble)
export(tidybulk)
export(tidybulk_SAM_BAM)
export(unnest)
exportMethods(as_SummarizedExperiment)
exportMethods(quantile_normalise_abundance)
exportMethods(scale_abundance)
exportMethods(tidybulk)
exportMethods(tidybulk_SAM_BAM)
import(SummarizedExperiment)
import(lifecycle)
import(methods)
import(parallel)
import(preprocessCore)
import(readr)
import(tibble)
importFrom(GenomicRanges,makeGRangesListFromDataFrame)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,t)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,as.data.frame)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(dplyr,across)
importFrom(dplyr,anti_join)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,contains)
importFrom(dplyr,count)
importFrom(dplyr,distinct)
importFrom(dplyr,do)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_drop_default)
importFrom(dplyr,group_cols)
importFrom(dplyr,if_else)
importFrom(dplyr,inner_join)
importFrom(dplyr,join_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,setdiff)
importFrom(dplyr,slice)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_all)
importFrom(dplyr,ungroup)
importFrom(lifecycle,deprecate_soft)
importFrom(lifecycle,deprecate_warn)
importFrom(magrittr,"%$%")
importFrom(magrittr,"%>%")
importFrom(magrittr,divide_by)
importFrom(magrittr,equals)
importFrom(magrittr,extract2)
importFrom(magrittr,multiply_by)
importFrom(magrittr,set_colnames)
importFrom(magrittr,set_rownames)
importFrom(parallel,mclapply)
importFrom(purrr,as_mapper)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_dfc)
importFrom(purrr,map2_dfr)
importFrom(purrr,map_chr)
importFrom(purrr,map_dfr)
importFrom(purrr,map_int)
importFrom(purrr,map_lgl)
importFrom(purrr,reduce)
importFrom(purrr,when)
importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,dots_list)
importFrom(rlang,dots_values)
importFrom(rlang,enquo)
importFrom(rlang,enquos)
importFrom(rlang,flatten_if)
importFrom(rlang,inform)
importFrom(rlang,is_quosure)
importFrom(rlang,is_spliced)
importFrom(rlang,quo)
importFrom(rlang,quo_is_missing)
importFrom(rlang,quo_is_null)
importFrom(rlang,quo_is_symbol)
importFrom(rlang,quo_is_symbolic)
importFrom(rlang,quo_name)
importFrom(rlang,quo_set_env)
importFrom(rlang,quo_squash)
importFrom(rlang,set_names)
importFrom(scales,extended_breaks)
importFrom(scales,label_scientific)
importFrom(scales,log_breaks)
importFrom(scales,trans_new)
importFrom(stats,as.formula)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,kmeans)
importFrom(stats,lsfit)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,plogis)
importFrom(stats,prcomp)
importFrom(stats,qlogis)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,terms)
importFrom(stringi,stri_c)
importFrom(stringr,str_c)
importFrom(stringr,str_detect)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_subset)
importFrom(tibble,as_tibble)
importFrom(tibble,enframe)
importFrom(tibble,rowid_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,complete)
importFrom(tidyr,drop_na)
importFrom(tidyr,gather)
importFrom(tidyr,nest)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyselect,any_of)
importFrom(ttservice,bind_cols)
importFrom(ttservice,bind_rows)
importFrom(utils,capture.output)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,install.packages)
importFrom(utils,packageDescription)
importFrom(utils,tail)
