VanAndelInstitute · ttriche · Nov 15, 2021 · Nov 15, 2021 · Nov 15, 2021 · Nov 15, 2021
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,8 +11,8 @@ Description: For the practical sessions in Experimental Design & Biostats 2021,
              Rstudio to \url{https://rpubs.com/}, so all that's left is to make
              sure that dependencies for assignments are in place. This package
              also includes a few convenience functions (phelp, lsos, etc.).
-Version: 0.11.15
-Date: 2021-11-15
+Version: 0.11.20
+Date: 2021-11-20
 Authors@R: person("Triche", "Lab", role=c("aut", "cre"), email="trichelab@gmail.com")
 Author: Triche Lab [aut, cre]
 Maintainer: Triche Lab <trichelab@gmail.com>
@@ -23,6 +23,7 @@ Depends:
     R (>= 4.0.0),
     conflicted,
     ggforce,
+    gtools,
     googlesheets4,
     moderndive,
     tidyverse,
@@ -31,13 +32,15 @@ Imports:
     BiocManager,
     broom,
     broom.mixed,
+    coefplot,
     corrr,
     datasets,
     devtools,
     dials,
     downlit,
     dplyr,
     factoextra,
+    forcats, 
     ggforce,
     ggplot2,
     ggthemes,
@@ -67,11 +70,15 @@ Imports:
     rpart,
     rpart.plot,
     rsample,
+    scater,
     scico,
+    SingleCellExperiment,
     skeletor,
     skimr,
+    SummarizedExperiment,
     tibble,
     tidyr,
+    tidySingleCellExperiment,
     tidytext,
     tidyverse,
     tune, 

diff --git a/vignettes/figure/SingleCellExperiment.png b/vignettes/figure/SingleCellExperiment.png
diff --git a/vignettes/figure/SummarizedExperiment.jpg b/vignettes/figure/SummarizedExperiment.jpg
diff --git a/vignettes/project2.Rmd b/vignettes/project2.Rmd
@@ -110,7 +110,7 @@ library(tidyverse)
 tibble(name = cells) %>% # stringr::str_split takes strings and a split pattern
   mutate(experiment = str_split(name, "\\.", simplify=TRUE)[,1]) %>% # column 1
   mutate(method = str_split(name, "\\.", simplify=TRUE)[,2]) %>% # column 2 
-  mutate(cell = str_split(name, "\\.", simplify=TRUE)[,3]) -> # column 3
+  mutate(barcode = str_split(name, "\\.", simplify=TRUE)[,3]) -> # column 3
     celltibble # the result is assigned to the object `celltibble`
 
 # how many cells per mixture were run with each method?
@@ -328,7 +328,7 @@ if (FALSE) { # if you want to recreate the SingleCellExperiment:
 }
 
 # if you just want to load it 
-tidybarnyard <- tidy(readRDS(url("https://ttriche.github.io/RDS/barnyard.rds")))
+tidybarnyard <- readRDS(url("https://ttriche.github.io/RDS/tidybarnyard.rds"))
 show(tidybarnyard)
 
 ```

diff --git a/vignettes/project2_chunks/figure/CITEseq.png b/vignettes/project2_chunks/figure/CITEseq.png
diff --git a/vignettes/project2_chunks/figure/UMAP.png b/vignettes/project2_chunks/figure/UMAP.png
diff --git a/vignettes/project2_chunks/figure/byMethod-1.png b/vignettes/project2_chunks/figure/byMethod-1.png
diff --git a/vignettes/project2_chunks/figure/bygenome-1.png b/vignettes/project2_chunks/figure/bygenome-1.png
diff --git a/vignettes/project2_chunks/figure/coefficients-1.png b/vignettes/project2_chunks/figure/coefficients-1.png
diff --git a/vignettes/project2_chunks/figure/coefficients-2.png b/vignettes/project2_chunks/figure/coefficients-2.png
diff --git a/vignettes/project2_chunks/figure/coefficients-3.png b/vignettes/project2_chunks/figure/coefficients-3.png
diff --git a/vignettes/project2_chunks/figure/coefficients-4.png b/vignettes/project2_chunks/figure/coefficients-4.png
diff --git a/vignettes/project2_chunks/figure/competitive-1.png b/vignettes/project2_chunks/figure/competitive-1.png
diff --git a/vignettes/project2_chunks/figure/confidenceintervals-1.png b/vignettes/project2_chunks/figure/confidenceintervals-1.png
diff --git a/vignettes/project2_chunks/figure/doubletgate-1.png b/vignettes/project2_chunks/figure/doubletgate-1.png
diff --git a/vignettes/project2_chunks/figure/gating-1.png b/vignettes/project2_chunks/figure/gating-1.png
diff --git a/vignettes/project2_chunks/figure/mixlabeledplot-1.png b/vignettes/project2_chunks/figure/mixlabeledplot-1.png
diff --git a/vignettes/project2_chunks/figure/mixlabels-1.png b/vignettes/project2_chunks/figure/mixlabels-1.png
diff --git a/vignettes/project2_chunks/figure/mixtureModel-1.png b/vignettes/project2_chunks/figure/mixtureModel-1.png
diff --git a/vignettes/project2_chunks/figure/ordered_sinaplot-1.png b/vignettes/project2_chunks/figure/ordered_sinaplot-1.png
diff --git a/vignettes/project2_chunks/figure/pullrequest.png b/vignettes/project2_chunks/figure/pullrequest.png
diff --git a/vignettes/project2_chunks/figure/remix-1.png b/vignettes/project2_chunks/figure/remix-1.png
diff --git a/vignettes/project2_chunks/figure/remix-2.png b/vignettes/project2_chunks/figure/remix-2.png
diff --git a/vignettes/project2_chunks/figure/remix-3.png b/vignettes/project2_chunks/figure/remix-3.png
diff --git a/vignettes/project2_chunks/figure/rowDataAndColumnData-1.png b/vignettes/project2_chunks/figure/rowDataAndColumnData-1.png
diff --git a/vignettes/project2_chunks/figure/sinaplot-1.png b/vignettes/project2_chunks/figure/sinaplot-1.png