Merge branch 'master' into unnest_SE

Author: stemangiola

.gitignore

@@ -15,3 +15,5 @@ dev/*pdf
 dev/dplyr-master/*
 tidySummarizedExperiment.Rproj
 GDCdata
+/doc/
+/Meta/

DESCRIPTION

@@ -1,15 +1,23 @@
 Type: Package
 Package: tidySummarizedExperiment
 Title: Brings SummarizedExperiment to the Tidyverse 
-Version: 1.9.6
+Version: 1.11.1
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
-Description: tidySummarizedExperiment is an adapter that abstracts the 'SummarizedExperiment' container 
-    in the form of tibble and allows the data manipulation, plotting and nesting using 'tidyverse' 
+Description: The tidySummarizedExperiment package provides a set of tools for creating and
+  manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment
+  is a widely used data structure in bioinformatics for storing high-throughput genomic data, 
+  such as gene expression or DNA sequencing data. 
+  The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. 
+  It allows users to convert their data into a tidy format, where each observation is a row 
+  and each variable is a column. This tidy representation simplifies data manipulation, 
+  integration with other tidyverse packages, and enables seamless integration with the broader 
+  ecosystem of tidy tools for data analysis.
 License: GPL-3
 Depends:
     R (>= 4.1.0),
-    SummarizedExperiment
+    SummarizedExperiment,
+    ttservice
 Imports:
     tibble (>= 3.0.4),
     dplyr,
@@ -29,7 +37,8 @@ Imports:
     pillar,
     stringr,
     cli,
-    fansi
+    fansi,
+    stats
 Suggests:
     BiocStyle,
     testthat,

NAMESPACE

@@ -1,12 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as_tibble,SummarizedExperiment)
+S3method(bind_cols,RangedSummarizedExperiment)
 S3method(bind_cols,SummarizedExperiment)
-S3method(bind_cols,default)
 S3method(bind_rows,SummarizedExperiment)
-S3method(bind_rows,default)
 S3method(count,SummarizedExperiment)
-S3method(count,default)
 S3method(distinct,SummarizedExperiment)
 S3method(extract,SummarizedExperiment)
 S3method(filter,SummarizedExperiment)
@@ -38,8 +36,8 @@ S3method(tidy,SummarizedExperiment)
 S3method(unite,SummarizedExperiment)
 S3method(unnest,tidySummarizedExperiment_nested)
 export("%>%")
+export()
 export(as_tibble)
-export(bind_cols)
 export(bind_rows)
 export(count)
 export(distinct)
@@ -70,8 +68,6 @@ export(tidy)
 export(unite)
 export(unnest)
 export(unnest_summarized_experiment)
-import(dplyr)
-import(tidyr)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
@@ -92,6 +88,8 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
+importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_drop_default)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -145,6 +143,7 @@ importFrom(rlang,names2)
 importFrom(rlang,quo_is_null)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)
@@ -163,5 +162,7 @@ importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(tidyselect,one_of)
+importFrom(ttservice,bind_cols)
+importFrom(ttservice,bind_rows)
 importFrom(utils,tail)
 importFrom(vctrs,new_data_frame)