undoing changes to the main repo

tidyomics · Jul 6, 2023 · 60c646e · 60c646e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tidyomicsWorkshop
 Title: Tidy genomic and transcriptomic analyses 
-Version: 0.16.2
+Version: 0.16.3
 Authors@R: 
     c(
     person(given = "Stefano",
@@ -31,6 +31,7 @@ Imports:
     tidySummarizedExperiment,
     tidySingleCellExperiment,
     tidygate,
+    tidyseurat,
     stats,
     utils,
     tibble,
@@ -52,6 +53,7 @@ Imports:
     dittoSeq,
     tidybulk,
     glue,
+    SeuratWrappers,
     scater,
     batchelor
 Suggests:

diff --git a/R/data_transcriptomics.R b/R/data_transcriptomics.R
@@ -1,29 +1,29 @@
-## #' seurat_obj
-## #'
-## #' A Seurat dataset of single cell RNA sequencing data
-## #'
-## #'
-## #' @format  A Seurat object.
-## #' @usage data(seurat_obj)
-## "seurat_obj"
+#' seurat_obj
+#'
+#' A Seurat dataset of single cell RNA sequencing data
+#'
+#'
+#' @format  A Seurat object.
+#' @usage data(seurat_obj)
+"seurat_obj"
 
-## #' gate_seurat_obj
-## #'
-## #' Coordinates for a gate interactively drawn using tidygate
-## #'
-## #'
-## #' @format  A list containing x,y coordinates for one gate
-## #' @usage data(gate_seurat_obj)
-## "gate_seurat_obj"
+#' gate_seurat_obj
+#'
+#' Coordinates for a gate interactively drawn using tidygate
+#'
+#'
+#' @format  A list containing x,y coordinates for one gate
+#' @usage data(gate_seurat_obj)
+"gate_seurat_obj"
 
-## #' seurat_obj_UMAP3
-## #'
-## #' A Seurat dataset of single cell RNA sequencing data with 3 UMAP dimesions
-## #'
-## #'
-## #' @format  A Seurat object.
-## #' @usage data(seurat_obj_UMAP3)
-## "seurat_obj_UMAP3"
+#' seurat_obj_UMAP3
+#'
+#' A Seurat dataset of single cell RNA sequencing data with 3 UMAP dimesions
+#'
+#'
+#' @format  A Seurat object.
+#' @usage data(seurat_obj_UMAP3)
+"seurat_obj_UMAP3"
 
 #' pseudo_bulk
 #'

diff --git a/seurat_data/gate_seurat_obj.rda → data/gate_seurat_obj.rda b/seurat_data/gate_seurat_obj.rda → data/gate_seurat_obj.rda
diff --git a/seurat_data/seurat_obj.rda → data/seurat_obj.rda b/seurat_data/seurat_obj.rda → data/seurat_obj.rda
diff --git a/seurat_data/seurat_obj_UMAP3.rda → data/seurat_obj_UMAP3.rda b/seurat_data/seurat_obj_UMAP3.rda → data/seurat_obj_UMAP3.rda
diff --git a/vignettes/pseudobulk_transcriptomics.Rmd b/vignettes/pseudobulk_transcriptomics.Rmd
@@ -12,7 +12,7 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, eval = FALSE)
+knitr::opts_chunk$set(echo = TRUE)
 ```
 
 ## Instructors

diff --git a/vignettes/single_cell_seurat_transcriptomics.Rmd b/vignettes/single_cell_seurat_transcriptomics.Rmd
@@ -12,7 +12,7 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, eval = FALSE)
+knitr::opts_chunk$set(echo = TRUE)
 ```
 
 ## Instructors

diff --git a/vignettes/solutions_transcriptomics.Rmd b/vignettes/solutions_transcriptomics.Rmd
@@ -7,10 +7,6 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r message = FALSE}
 library(SingleCellExperiment)
 library(ggplot2)

diff --git a/vignettes/supplementary_transcriptomics.Rmd b/vignettes/supplementary_transcriptomics.Rmd
@@ -8,7 +8,7 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, eval = FALSE)
+knitr::opts_chunk$set(echo = TRUE)
 ```