Fixes

Gemfile

@@ -26,3 +26,4 @@ gem "jemoji"
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
 gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+

exercises.md

@@ -34,9 +34,10 @@ Snakemake pipeline for processing SmartSeq2 data.
 For those not familiar with working with biomaRt, we suggest that you have a look at this example code for how to convert between different formats using biomaRt. 
 
 *	[Tutorial for biomaRt](labs/biomart) 
-#### PCA and clustering
 
-Basic PCA and clustering using base R on mouse embryonic development data.
+#### PCA, tSNE and clustering
+
+Basic PCA, tSNE and clustering using base R on mouse embryonic development data.
 
 *	[Tutorial for PCA and clustering](labs/PCA_and_clustering)
 

index.md

@@ -6,6 +6,52 @@ title: Single cell RNA sequencing analysis course
 # Single cell RNA sequencing analysis course
 Scilifelab Solna, Rooms Air & Fire,  2018-05-21 - 2018-05-23
 
+{% highlight bash %}
+# check alignment of text
+asbd      ösjgödlkj
+ögkjlök   jgkldj
+kjk       llll
+ii        asg
+{% endhighlight %}
+
+``` r
+# test R code block
+nPlot <- 5 #number of genes top plot per pc.
+par(mfrow=c(5,2),mar=c(2,2,1,1),oma=c(1,5,1,1))
+for (i in 1:5) {
+    top<-order(PC$rotation[,i],decreasing=T)[1:nPlot]
+    bottom<-order(PC$rotation[,i],decreasing=F)[1:nPlot]
+    barplot(contr[top,i],main=sprintf("genes on pos axis PC%d",i),
+            ylab="% contr",las=2,horiz=T)
+    barplot(contr[bottom,i],main=sprintf("genes on neg axis PC%d",i),
+            ylab="% contr",las=2,horiz=T)
+}
+```
+
+{% highlight bash %}
+# Johan code block with 
+$ bundle exec jekyll serve
+mmmmm mmmmm
+lllll lllll
+{% endhighlight %}
+
+
+```js
+// Javascript code with syntax highlighting.
+var fun = function lang(l) {
+  dateformat.i18n = require('./lang/' + l)
+  return true;
+}
+```
+
+```ruby
+# Ruby code with syntax highlighting
+GitHubPages::Dependencies.gems.each do |gem, version|
+  s.add_dependency(gem, "= #{version}")
+end
+```
+
+
 
 ##### Schedule
 
@@ -15,6 +61,8 @@ Course schedule can be found here: [Schedule](schedule)
 
 All exercises for the afternoon sessions can be found at [Exercises](exercises). 
 
+For working on Uppmax: to use the allocations we have for the course, please look [here](login.md).
+
 ##### Precourse
 
 Please read carefully the [Precourse material](precourse) before the course start. 
@@ -27,4 +75,5 @@ Please read carefully the [Precourse material](precourse) before the course star
 ##### Course leaders
 
 * [Åsa Björklund](http://nbis.se/about/staff/asa-bjorklund/)
-* [Stefania Giacomello](http://nbis.se/about/staff/stefania-giacomello/)
+* [Stefania Giacomello](http://nbis.se/about/staff/stefania-giacomello/)
+

labs/PCA_and_clustering.Rmd

@@ -260,7 +260,7 @@ for (gene in plotgenes) {
 
 Now, lets try some different clustering methods. Quite often, clustering is based on pairwise correlations. So let's start with calculating pairwise correlations for all samples. Default for the R-function cor is Pearson correlation.
 
-```{r}
+```{r, warning=FALSE}
 C<-cor(log2(DATA+1))
 
 # Run clustering based on the correlations, where the distance will 
@@ -279,7 +279,7 @@ hcl.euk<-hclust(dist.euk,method="ward.D2")
 #Lets plot a heatmap with the correlations and the results from the different clustering methods. 
 # Here we use the dendrogram from hclust to order the cells.
 	
-library(gplots)
+suppressMessages(library(gplots))
 heatmap.2(C,ColSideColors=col.stage,RowSideColors=col.stage,
           Colv=as.dendrogram(hcl.corr),Rowv=as.dendrogram(hcl.corr),
           scale="none",trace="none",main="correlation, Ward")

labs/PCA_and_clustering.md

@@ -325,21 +325,7 @@ hcl.euk<-hclust(dist.euk,method="ward.D2")
 #Lets plot a heatmap with the correlations and the results from the different clustering methods. 
 # Here we use the dendrogram from hclust to order the cells.
 
-library(gplots)
-```
-
-    ## 
-    ## Attaching package: 'gplots'
-
-    ## The following object is masked from 'package:plotrix':
-    ## 
-    ##     plotCI
-
-    ## The following object is masked from 'package:stats':
-    ## 
-    ##     lowess
-
-``` r
+suppressMessages(library(gplots))
 heatmap.2(C,ColSideColors=col.stage,RowSideColors=col.stage,
           Colv=as.dendrogram(hcl.corr),Rowv=as.dendrogram(hcl.corr),
           scale="none",trace="none",main="correlation, Ward")

login.md

@@ -1,12 +1,12 @@
 ---
 layout: default
-title:  'Single cell RNA sequencing data analysis'
+title:  'login - scRNAseq course'
 ---
 
 
 # scRNAseq course
 
-Held in Uppsala October 2-4, 2017.
+Held in Solna May 21-23, 2018.
 
 ##  How to login on interactive node during exercise