remove sessionInfo output

_episodes/02-Experimental-Considerations.md

@@ -3,8 +3,8 @@
 # Instead, please edit 02-Experimental-Considerations.md in _episodes_rmd/
 source: Rmd
 title: "Experimental Considerations"
-teaching: 30
-exercises: 10
+teaching: 90
+exercises: 30
 questions:
 - "How do I design a rigorous and reproducible single cell RNAseq experiment?"
 objectives:
@@ -273,29 +273,3 @@ Mol Syst Biol [link](https://pubmed.ncbi.nlm.nih.gov/31217225/)
 sessionInfo()
 ~~~
 {: .language-r}
-
-
-
-~~~
-R version 4.1.0 (2021-05-18)
-Platform: x86_64-apple-darwin17.0 (64-bit)
-Running under: macOS Big Sur 10.16
-
-Matrix products: default
-BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
-LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
-
-locale:
-[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
-
-attached base packages:
-[1] stats     graphics  grDevices utils     datasets  methods   base     
-
-other attached packages:
-[1] knitr_1.41
-
-loaded via a namespace (and not attached):
-[1] compiler_4.1.0 magrittr_2.0.3 tools_4.1.0    stringi_1.7.8  stringr_1.4.1 
-[6] xfun_0.35      evaluate_0.18 
-~~~
-{: .output}

_episodes_rmd/02-Experimental-Considerations.Rmd

@@ -269,6 +269,6 @@ Mol Syst Biol [link](https://pubmed.ncbi.nlm.nih.gov/31217225/)
 
 ## Session Info
 
-```{r session_info}
+```{r session_info, eval=FALSE}
 sessionInfo()
 ```

_episodes_rmd/03-Overview-scRNA-seq-Data.Rmd

@@ -209,6 +209,11 @@ column in 'features.tsv.gz' as the gene identifier.
 
 Run the following command. This may take up to three minutes to complete.
 
+```{r set_working_dir, eval=FALSE}
+# first move into the scripts directory you created earlier
+setwd("scripts")
+```
+
 ```{r read_counts}
 # uses the Seurat function Read10X()
 counts <- Read10X(file.path(data_dir, 'mouseStSt_invivo'), gene.column = 1)
@@ -218,7 +223,7 @@ counts <- Read10X(file.path(data_dir, 'mouseStSt_invivo'), gene.column = 1)
 
 How many rows and columns are there in `counts`?
 
-```{r dim_counts}
+```{r dim_counts, message=FALSE}
 dim(counts)
 ```
 
@@ -357,7 +362,7 @@ The sample metadata file is a comma-separated variable (CSV) file, We will read
 it in using the readr 
 [read_csv](https://readr.tidyverse.org/reference/read_delim.html) function.
 
-```{r read_metadata}
+```{r read_metadata, message=FALSE}
 metadata <- read_csv(file.path(data_dir, 'mouseStSt_invivo', 'annot_metadata_first.csv'))
 ```
 
@@ -452,7 +457,7 @@ directory and save them to a file called 'lesson03_challenge.Rdata'.
 
 ### Session Info
 
-```{r session_info,collapse=TRUE}
+```{r session_info,collapse=TRUE, eval=FALSE}
 sessionInfo()
 ```
 

_episodes_rmd/04-Quality-Control.Rmd

@@ -635,6 +635,6 @@ Filter the Seurat object by mitochondrial gene expression.
 
 ## Session Info
 
-```{r session_info,collapse=TRUE}
+```{r session_info,collapse=TRUE, eval=FALSE}
 sessionInfo()
 ```

_episodes_rmd/05-Common-Analyses.Rmd

@@ -315,6 +315,6 @@ saveRDS(liver, file = file.path(data_dir, 'lesson05.rds'))
 
 ## Session Info
 
-```{r session_info}
+```{r session_info, eval=FALSE}
 sessionInfo()
 ```

setup.md

@@ -81,8 +81,6 @@ dir.create("results")
 
 **Before the workshop**, please download the following files:
 
-TBD: Users will download a subset of the counts and metadata from somewhere (Box?). So far, 25% of the full data from liveratlas.org seems to work well. 
-
 Open the `scRNA.Rproj` project.
 
 ~~~