Merge pull request #271 from stemangiola/drop-bind-generics

Drop bind generics

.gitignore

@@ -17,3 +17,4 @@ tidybulk.Rproj
 egsea_report_*
 /doc*
 /Meta/
+/doc/

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidybulk
 Title: Brings transcriptomics to the tidyverse 
-Version: 1.11.3
+Version: 1.11.4
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -12,7 +12,8 @@ Description: This is a collection of utility functions that allow
     a modular, pipe-friendly and tidy fashion.
 License: GPL-3
 Depends:
-    R (>= 4.1.0)
+    R (>= 4.1.0),
+    ttservice (>= 0.3.6)
 Imports:
     tibble,
     readr,
@@ -75,7 +76,9 @@ Suggests:
     uwot,
     matrixStats,
     igraph,
-    EGSEA
+    EGSEA,
+    IRanges,
+    here
 VignetteBuilder: 
     knitr
 RdMacros:

NAMESPACE

@@ -1,9 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(arrange,tidybulk)
-S3method(bind_cols,default)
 S3method(bind_cols,tidybulk)
-S3method(bind_rows,default)
 S3method(bind_rows,tidybulk)
 S3method(distinct,tidybulk)
 S3method(filter,tidybulk)
@@ -28,7 +26,6 @@ export(as_SummarizedExperiment)
 export(as_matrix)
 export(as_tibble)
 export(bind_cols)
-export(bind_rows)
 export(cluster_elements)
 export(deconvolve_cellularity)
 export(describe_transcript)
@@ -59,6 +56,7 @@ export(right_join)
 export(rotate_dimensions)
 export(rowwise)
 export(scale_abundance)
+export(select)
 export(summarise)
 export(symbol_to_entrez)
 export(test_differential_abundance)
@@ -71,15 +69,17 @@ export(tibble)
 export(tidybulk)
 export(tidybulk_SAM_BAM)
 export(unnest)
+exportMethods(as_SummarizedExperiment)
+exportMethods(scale_abundance)
+exportMethods(tidybulk)
+exportMethods(tidybulk_SAM_BAM)
 import(SummarizedExperiment)
-import(dplyr)
 import(lifecycle)
 import(methods)
 import(parallel)
 import(preprocessCore)
 import(readr)
 import(tibble)
-import(tidyr)
 importFrom(GenomicRanges,makeGRangesListFromDataFrame)
 importFrom(S4Vectors,metadata)
 importFrom(SummarizedExperiment,SummarizedExperiment)
@@ -88,21 +88,34 @@ importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
 importFrom(dplyr,across)
+importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)
-importFrom(dplyr,bind_rows)
+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,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_if)
+importFrom(dplyr,n)
+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)
@@ -129,6 +142,7 @@ 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_spliced)
@@ -160,6 +174,7 @@ importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stats,terms)
 importFrom(stringi,stri_c)
+importFrom(stringr,str_detect)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
@@ -169,12 +184,18 @@ 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,one_of)
+importFrom(ttservice,bind_cols)
+importFrom(ttservice,bind_rows)
 importFrom(utils,capture.output)
 importFrom(utils,data)
 importFrom(utils,head)

R/data.R

@@ -53,11 +53,6 @@
 #'
 "breast_tcga_mini_SE"
 
-#' Needed for vignette counts_SE
-#'
-#'
-"counts_SE"
-
 #' Needed for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta
 #'
 #'