clean all files for for Bioconductor submission

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidytof
 Title: Analyze High-dimensional Cytometry Data Using Tidy Data Principles
-Version: 0.0.0
+Version: 0.99.0
 Authors@R: 
     c(person(given = "Timothy",
              family = "Keyes",
@@ -16,16 +16,16 @@ Authors@R:
              family = "Nolan", 
              role = c("rth", "own"), 
              email = "[email protected]"))    
-Description: An interactive scientific data analysis pipeline for high-dimensional
-    cytometry data built using tidy data principles.  It is
-    specifically designed to play well with the tidyverse suite of data
-    cleaning and analysis tools, with functionality for reading/writing data
-    files, data cleaning, preprocessing, clustering,
-    visualization, modeling, and other quality-of-life functions. Implements a 
-    "grammar" of single-cell data analysis.
+Description: This package implements an interactive, scientific analysis
+    pipeline for high-dimensional cytometry data built using tidy data principles.  
+    It is specifically designed to play well with both the tidyverse and 
+    Bioconductor software ecosystems, with functionality for reading/writing 
+    data files, data cleaning, preprocessing, clustering,
+    visualization, modeling, and other quality-of-life functions. tidytof 
+    implements a "grammar" of high-dimensional cytometry data analysis.
 License: MIT + file LICENSE
 Depends: 
-    R (>= 4.1)
+    R (>= 4.3)
 Imports:
     doParallel,
     dplyr,
@@ -40,7 +40,6 @@ Imports:
     readr,
     recipes,
     rlang,
-    rsample,
     stringr,
     survival,
     tidygraph,
@@ -80,15 +79,16 @@ Suggests:
     SingleCellExperiment,
     Seurat,
     SeuratObject,
-    embed
+    embed,
+    rsample
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 LinkingTo: 
     Rcpp
 URL: https://keyes-timothy.github.io/tidytof,
     https://keyes-timothy.github.io/tidytof/
 VignetteBuilder: knitr
 Language: en-US
-biocViews: SingleCellWorkflow
+biocViews: SingleCell, FlowCytometry

NAMESPACE

@@ -221,16 +221,9 @@ importFrom(readr,cols)
 importFrom(readr,read_csv)
 importFrom(readr,write_csv)
 importFrom(recipes,all_numeric)
-importFrom(recipes,all_numeric_predictors)
-importFrom(recipes,all_predictors)
-importFrom(recipes,bake)
 importFrom(recipes,juice)
 importFrom(recipes,prep)
-importFrom(recipes,prepper)
 importFrom(recipes,recipe)
-importFrom(recipes,step_dummy)
-importFrom(recipes,step_impute_knn)
-importFrom(recipes,step_nzv)
 importFrom(recipes,step_pca)
 importFrom(rlang,`.data`)
 importFrom(rlang,`:=`)
@@ -244,11 +237,6 @@ importFrom(rlang,ensym)
 importFrom(rlang,is_installed)
 importFrom(rlang,quo)
 importFrom(rlang,sym)
-importFrom(rsample,bootstraps)
-importFrom(rsample,initial_split)
-importFrom(rsample,testing)
-importFrom(rsample,training)
-importFrom(rsample,vfold_cv)
 importFrom(stats,C)
 importFrom(stats,as.formula)
 importFrom(stats,cor)

NEWS.md

@@ -0,0 +1,13 @@
+# tidytof 0.99.0
+
+NEW FEATURES
+
+* Added a `NEWS.md` file to track changes to the package.
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* Submitted to Bioconductor
+
+BUG FIXES
+
+* None