move Bioconductor library install and load instructions to the setup …

…page

episodes/differential-expression-analysis.Rmd

@@ -24,24 +24,6 @@ exercises: 10
 # Differential Expression Analysis
 
 ```{r, echo=FALSE}
-# When the following query arises, type 'a'
-# Update all/some/none? [a/s/n]: a
-
-# When the following query arises, type 'n' (it is faster)
-# Do you want to install from sources the packages which need compilation? 
-# (Yes/no/cancel) n
-
-if (!requireNamespace("BiocManager", quietly = TRUE))
-
-    install.packages("BiocManager")
-
-BiocManager::install("clusterProfiler")
-BiocManager::install("DESeq2")
-BiocManager::install("AnnotationDbi")
-BiocManager::install("org.Mm.eg.db")
-BiocManager::install("org.Hs.eg.db")
-BiocManager::install("GO.db")
-BiocManager::install("EnhancedVolcano")
 suppressPackageStartupMessages(library("clusterProfiler"))
 suppressPackageStartupMessages(library("DESeq2"))
 suppressPackageStartupMessages(library("AnnotationDbi"))

episodes/exploring-data-in-synapse.Rmd

@@ -71,8 +71,8 @@ rows in a nice tidy output. Doing the same for a base R dataframe read in with
 to inspect a large dataframe, use `head(df)` to view the first several rows 
 only.
 
-```{r, counts_tibble}
-kable(counts)
+```{r, counts_tibble, results='asis'}
+counts
 ```
 
 The data file has a column of ENSEMBL `gene_id`s and then a bunch of columns 

learners/setup.md

@@ -31,16 +31,49 @@ install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fh
 install.packages("tidyverse")
 install.packages("dplyr")
 install.packages("lubridate")
+
+# load the 4 libraries you just installed
+library(synapser)
+library("tidyverse")
+library("dplyr")
+library("lubridate")
+```
+
+Install Bioconductor packages.
+
+```
+
+# When the following query arises, type 'a'
+# Update all/some/none? [a/s/n]: a
+
+# When the following query arises, type 'n' (it is faster)
+# Do you want to install from sources the packages which need compilation? 
+# (Yes/no/cancel) n
+
+if (!requireNamespace("BiocManager", quietly = TRUE))
+
+    install.packages("BiocManager")
+
+BiocManager::install("clusterProfiler")
+BiocManager::install("DESeq2")
+BiocManager::install("AnnotationDbi")
+BiocManager::install("org.Mm.eg.db")
+BiocManager::install("org.Hs.eg.db")
+BiocManager::install("GO.db")
+BiocManager::install("EnhancedVolcano")
 ```
 
 Once the installation has finished, copy and paste the following commands into 
 the console to verify that packages installed correctly.
 
-```r
-library(synapser)
-library(tidyverse)
-library(dplyr)
-library(lubridate)
+```
+library("clusterProfiler")
+library("DESeq2")
+library("AnnotationDbi")
+library("org.Mm.eg.db")
+library("org.Hs.eg.db")
+library("GO.db")
+library("EnhancedVolcano")
 ```
 
 Next, you will need to log in to your Synapse account.
@@ -97,13 +130,13 @@ BiocManager::install("GO.db")
 BiocManager::install("EnhancedVolcano")
 ```
 ```r
-suppressPackageStartupMessages(library("DESeq2"))
-suppressPackageStartupMessages(library("AnnotationDbi"))
-suppressPackageStartupMessages(library("org.Mm.eg.db"))
-suppressPackageStartupMessages(library("org.Hs.eg.db"))
-suppressPackageStartupMessages(library("GO.db"))
-suppressPackageStartupMessages(library("EnhancedVolcano"))
-suppressPackageStartupMessages(library("clusterProfiler"))
+library("DESeq2"))
+library("AnnotationDbi"))
+library("org.Mm.eg.db"))
+library("org.Hs.eg.db"))
+library("GO.db"))
+library("EnhancedVolcano"))
+library("clusterProfiler"))
 ```
 
 ## Project Setup