Extending de templates

.gitignore

@@ -13,3 +13,9 @@ docs
 /doc/
 /Meta/
 .DS*
+inst/rmarkdown/templates/rnaseq/skeleton/DE/Multiplicative_DGE_Analysis.Rmd
+tests/*
+.Rdata
+.httr-oauth
+.DS_Store
+.quarto

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.1.3
+Version: 0.2.0
 Authors@R: person("Pantano", "Lorena", , "[email protected]",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
@@ -20,8 +20,13 @@ Imports:
     grDevices,
     R.utils,
     readr,
+    withr,
+    usethis,
     fs,
-    withr
+    jsonlite,
+    yaml,
+    whisker,
+    rlang
 Suggests: 
     knitr,
     rmarkdown,
@@ -30,4 +35,4 @@ VignetteBuilder: knitr
 URL: http://bcb.io/bcbioR/
 Config/testthat/edition: 3
 Depends: 
-    R (>= 2.10)
+    R (>= 4.3.1)

NAMESPACE

@@ -1,18 +1,21 @@
 # Generated by roxygen2: do not edit by hand
 
 export(bcbio_nfcore_check)
-export(bcbio_set_project)
 export(bcbio_templates)
 export(cb_friendly_cols)
 export(cb_friendly_pal)
 export(list_cb_friendly_cols)
 export(scale_color_cb_friendly)
 export(scale_fill_cb_friendly)
+export(use_bcbio_analysis)
+export(use_bcbio_projects)
 import(DESeq2)
 import(R.utils)
+import(fs)
 import(ggplot2)
 import(ggprism)
 import(hues)
+import(usethis)
 importFrom(grDevices,colorRampPalette)
 importFrom(magrittr,"%>%")
 importFrom(readr,read_csv)

R/bcbioR-package.R

@@ -9,6 +9,8 @@
 ## usethis namespace: end
 #' @import DESeq2
 #' @import ggplot2
+#' @import usethis
+#' @import fs
 #' @import hues
 #' @import ggprism
 #' @import R.utils