Merge pull request #331 from stemangiola/v2

V2

Author: stemangiola

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^vignettes/introduction_cache$
@@ -13,4 +15,7 @@ README.Rmd
 .travis.yml
 .RData
 ^\.github$
-^_pkgdown.yml
+^_pkgdown.yml
+^egsea_report*
+^vignettes/egsea*
+^tests/testthat/egsea*

.gitignore

@@ -23,3 +23,11 @@ _targets*
 .DS_Store
 ._.DS_Store
 counts_SE.rda
+R/rotate_dimensions.R
+renv/.gitignore
+renv/activate.R
+renv/settings.json
+.Rprofile
+tidybulk.Rcheck/*
+..Rcheck/*
+vignettes/cache/*

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidybulk
 Title: Brings transcriptomics to the tidyverse 
-Version: 1.21.1
+Version: 1.99.2
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -16,16 +16,13 @@ Depends:
     ttservice (>= 0.3.6)
 Imports:
     tibble,
-    readr,
     dplyr (>= 1.1.0),
     magrittr,
     tidyr,
-    stringi,
     stringr,
     rlang,
     purrr,
     tidyselect,
-    preprocessCore,
     stats,
     parallel,
     utils,
@@ -76,6 +73,7 @@ Suggests:
     markdown,
     uwot,
     matrixStats,
+    preprocessCore,
     igraph,
     EGSEA,
     IRanges,
@@ -86,7 +84,10 @@ Suggests:
     lme4,
     glmmTMB,
     MASS,
-    pkgconfig
+    pkgconfig,
+    enrichplot,
+    patchwork,
+    airway
 VignetteBuilder: 
     knitr
 RdMacros:

NAMESPACE

@@ -1,114 +1,75 @@
 # 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("%>%")
+S3method(tidybulk::filterByExpr,DGEList)
+S3method(tidybulk::filterByExpr,default)
+S3method(validation,default)
+S3method(validation,tidybulk)
 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_differential_expression)
 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(S4Vectors,DataFrame)
+importFrom(S4Vectors,as.data.frame)
 importFrom(S4Vectors,metadata)
+importFrom(SummarizedExperiment,"assays<-")
+importFrom(SummarizedExperiment,"colData<-")
+importFrom(SummarizedExperiment,"rowData<-")
+importFrom(SummarizedExperiment,"rowRanges<-")
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,as.data.frame)
+importFrom(SummarizedExperiment,assay)
+importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,colnames)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
+importFrom(crayon,blue)
 importFrom(dplyr,across)
-importFrom(dplyr,anti_join)
+importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
+importFrom(dplyr,as_tibble)
 importFrom(dplyr,between)
-importFrom(dplyr,contains)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
 importFrom(dplyr,count)
+importFrom(dplyr,desc)
 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)
@@ -119,7 +80,6 @@ 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)
@@ -132,35 +92,35 @@ 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,not)
 importFrom(magrittr,set_colnames)
 importFrom(magrittr,set_rownames)
+importFrom(methods,is)
+importFrom(methods,new)
+importFrom(methods,slot)
+importFrom(parallel,clusterExport)
+importFrom(parallel,makeCluster)
 importFrom(parallel,mclapply)
-importFrom(purrr,as_mapper)
+importFrom(parallel,parLapply)
+importFrom(parallel,stopCluster)
 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)
@@ -174,11 +134,17 @@ importFrom(scales,extended_breaks)
 importFrom(scales,label_scientific)
 importFrom(scales,log_breaks)
 importFrom(scales,trans_new)
+importFrom(stats,AIC)
+importFrom(stats,anova)
 importFrom(stats,as.formula)
+importFrom(stats,coef)
 importFrom(stats,cor)
 importFrom(stats,cov)
 importFrom(stats,dist)
+importFrom(stats,hat)
 importFrom(stats,kmeans)
+importFrom(stats,lm)
+importFrom(stats,logLik)
 importFrom(stats,lsfit)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
@@ -187,39 +153,40 @@ importFrom(stats,p.adjust)
 importFrom(stats,pchisq)
 importFrom(stats,plogis)
 importFrom(stats,prcomp)
+importFrom(stats,predict)
 importFrom(stats,qlogis)
 importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,terms)
-importFrom(stringi,stri_c)
+importFrom(stats,update.formula)
+importFrom(stats,vcov)
 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,all_of)
 importFrom(tidyselect,any_of)
-importFrom(ttservice,bind_cols)
-importFrom(ttservice,bind_rows)
+importFrom(tidyselect,ends_with)
 importFrom(utils,capture.output)
+importFrom(utils,combn)
 importFrom(utils,data)
 importFrom(utils,head)
 importFrom(utils,install.packages)
 importFrom(utils,packageDescription)
+importFrom(utils,packageVersion)
 importFrom(utils,tail)