adds icon references

exercises.md

@@ -61,3 +61,5 @@ We will try to keep these tutorials up to date. If you find any errors or things
 As you run into problems, we will try to fill in the [FAQ](labs/FAQ) with common questions.
 
 <br/>
+
+<div style="text-align: right; font-size: 5px"> Icons are provided from [www.svgrepo.com](www.svgrepo.com) </div>

index.md

@@ -40,7 +40,7 @@ On the fourth day we offer a "Bring your own data" day where you can analyse you
 
 ###### How to apply
 
-Fill in this [application](https://forms.gle/6VFVTFep6iYk7wLr9) by December 16th and please indicate whether you are planning to participate on the optional day of January 30th. 
+Fill in this [application](https://forms.gle/6VFVTFep6iYk7wLr9) by December 16th and please indicate whether you are planning to participate on the optional day of January 30th.
 
 ###### Course fee
 
@@ -83,7 +83,7 @@ For working on Uppmax: to use the allocations we have for the course, please loo
 ##### <img border="0" src="https://www.svgrepo.com/show/19652/maths-class-materials-cross-of-a-pencil-and-a-ruler.svg" width="40" height="40"> Precourse material
 ***
 
-Please read carefully the [Precourse material](precourse.md) before the course start. 
+Please read carefully the [Precourse material](precourse.md) before the course start.
 
 <br/>
 
@@ -113,7 +113,7 @@ If you have any questions regarding the course, please email to Åsa Björklund
 * [Repository listing many scRNA-seq tools](https://github.com/seandavi/awesome-single-cell)
 * [SingleCellExperiment objects for many datasets](https://hemberg-lab.github.io/scRNA.seq.datasets/)
 * [Conquer datasets - many different datasets based on a salmon pipeline](http://imlspenticton.uzh.ch:3838/conquer/)
-* [The Human Cell Atlas project](https://www.humancellatlas.org/) 
+* [The Human Cell Atlas project](https://www.humancellatlas.org/)
 * [The github repository for this course. Also contains the R markdown scripts that was used to generate all the exercises](https://github.com/NBISweden/workshop-scRNAseq)
 * [Bitbucket repository for QC report scripts](https://bitbucket.org/asbj/qc-summary_scrnaseq)
 * [Bitbucket repository for the NBIS scRNAseq pipeline](https://bitbucket.org/scilifelab-lts/lts-workflows-sm-scrnaseq)
@@ -127,3 +127,6 @@ If you have any questions regarding the course, please email to Åsa Björklund
 * [Stockholm May 21-23, 2018](https://nbisweden.github.io/workshop-archive/workshop-scRNAseq/2018-05-21/)
 * [Uppsala October 2-4, 2017](https://scilifelab.github.io/courses/scrnaseq/1710/)
 
+<br/>
+
+<div style="text-align: right; font-size: 5px"> Icons are provided from [www.svgrepo.com](www.svgrepo.com) </div>

precourse.md

@@ -63,3 +63,7 @@ Or download manually from the github site https://github.com/NBISweden/workshop-
 4.   If you still feel uncertain how to work in a terminal please take time to do the first three parts in the “Unix tutorial for beginners” that can be found here http://www.ee.surrey.ac.uk/Teaching/Unix/ before the course starts. Otherwise you will not be able to take in the practical parts.  
 
 5.   Make sure that you can read and write in the course folder by creating a file with your uppmax user name in the `/proj/g2019002/completed` folder. If you cannot write to the folder, the most likely reason is that you have not requested access to the course project via [SUPR](https://supr.snic.se/), see point 2. OBS! It may take an hour or so from the time your access is approved before you can actually write to the folder. We will check before the course that all students have logged in and done this, so do not forget!
+
+<br/>
+
+<div style="text-align: right; font-size: 5px"> Icons are provided from [www.svgrepo.com](www.svgrepo.com) </div>

schedule.md

@@ -14,38 +14,38 @@ Lecture slides will be provided as links as they get completed.
 
 <br/>
 
-**Monday 27th of January**  
+###### Monday 27th of January
 
 | Time  | Description         | Lecturer  |
 | ----- | ------------------- | --------- |
 | 09.00 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Course introduction](slides2019/course_intro_Asa_Bjorklund_2019.pdf) | Åsa Björklund |
 | 09.15 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [scRNAseq methodologies and ESCG platform](slides2019/Eukaryotic_Single_Cell_Transcriptomics_HG_2019.pdf) | Karolina Wallenborg |
-| 10.00 | ** Coffee Break **	| |
-| 10.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [scRNAseq Quality Control] | <a href="slides2019/scRNAseq_QC_Asa_Bjorklund_2019.pdf"><img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"></a> | Åsa Björklund |
+| 10.00 | **Coffee Break**	| |
+| 10.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [scRNAseq Quality Control](slides2019/scRNAseq_QC_Asa_Bjorklund_2019.pdf) | Åsa Björklund |
 | 10.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Data normalization](slides2019/read_alignments_2019_J_Reimegard.pdf) | Åsa / Nikolay |
-| 12.10 | ** Lunch ** | |
+| 12.10 | **Lunch** | |
 | 13.15 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Intro to exercises](slides2019/exercises_intro_Asa_Bjorklund_2019.pdf) | Åsa Björklund |
 | 13.30 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Quality control](exercises.md) | Åsa, Paulo, Nikolay |
-| 15.00 | ** Coffee Break **	| |
+| 15.00 | **Coffee Break**	| |
 | 15.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Dimensionality reduction](slides2019/Dimensionality_reduction_P_Czarnewski_2019.pdf) | Paulo Czarnewski |   
 | 16.30 | [Wrap up of todays lectures](https://goo.gl/forms/fr3owaquQgo72E2K3) | Åsa Björklund  |
 
 <br/>
 
 <br/>
 
-**Tuesday 28th of January**  
+###### Tuesday 28th of January
 
 | Time  | Description         | Lecturer  |
 | ----- | ------------------- | --------- |
 | 09.00 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Dimensionality reduction](exercises.md) | Åsa, Paulo |
-| 10.00 | ** Coffee Break **	| |
+| 10.00 | **Coffee Break**	| |
 | 10.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> Batch correction + Data integration | Paulo Czarnewski |   
 | 09.00 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Data integration](exercises.md) | Åsa, Paulo |
-| 12.00 | ** Lunch ** | |
-| 13.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Clustering techniques and scRNAseq toolkits](slides2019/scRNAseq_toolkits_Asa_Bjorklund_2019.pdf) | Paulo Czarnewski |   
+| 12.00 | **Lunch** | |
+| 13.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Clustering techniques and scRNAseq toolkits](slides2019/scRNAseq_toolkits_Asa_Bjorklund_2019.pdf) | Åsa Björklund |   
 | 09.00 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Clustering](exercises.md) | Åsa, Paulo |
-| 10.00 | ** Coffee Break **	| |
+| 10.00 | **Coffee Break**	| |
 | 09.00 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Clustering (continued)](exercises.md) | Åsa, Paulo |
 | 16.30 | [Wrap up of todays lectures](https://goo.gl/forms/vDBBZrSyExz3Lh4K2) | Åsa Björklund  |
 | 18.00 | ** Course dinner at [Grappa](http://www.grappabar.nu) ** |
@@ -54,37 +54,38 @@ Lecture slides will be provided as links as they get completed.
 
 <br/>
 
-**Wednesday 29th of January**  
+###### Wednesday 29th of January  
 
 | Time  | Description         | Lecturer  |
 | ----- | ------------------- | --------- |
 | 09.00 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> Differential expression | Paulo Czarnewski |   
-| 09.45 | ** Coffee Break ** | |
+| 09.45 | **Coffee Break** | |
 | 10.15 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Differential expression](exercises.md) | Åsa, Paulo |
 | 11.15 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> [Trajectory inference] | Paulo Czarnewski |   
-| 12.00 | ** Lunch ** | |
+| 12.00 | **Lunch** | |
 | 13.00 | <img border="0" src="https://www.svgrepo.com/show/6672/exercise.svg" width="20" height="20"> [Exercises: Trajectory inference](exercises.md) | Paulo Czarnewski |
-| 14.00 | ** Coffee Break ** | |
-| 14.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.sv" width="20" height="20"> Invited seminar: Single-cell multi-omics  (Protein + RNA) | Johan Reimegård |
-| 15.15 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.sv" width="20" height="20"> Invited seminar: Spatial transcriptomics | Lars Borm |
+| 14.00 | **Coffee Break** | |
+| 14.30 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> Invited seminar: Single-cell multi-omics  (Protein + RNA) | Johan Reimegård |
+| 15.15 | <img border="0" src="https://www.svgrepo.com/show/165459/business-presentation.svg" width="20" height="20"> Invited seminar: Spatial transcriptomics | Lars Borm |
 | 16.00 | [Wrap up of todays lectures](https://goo.gl/forms/LabSH8u7S2IQVZKj1) | Åsa Björklund |
-| 16.15 | ** Course Summary ** | Åsa Björklund |
+| 16.15 | **Course Summary** | Åsa Björklund |
 
 <br/>
 
 <br/>
 
-**Wednesday 30th of January**  
+###### Wednesday 30th of January  
 
 | Time  | Description         | Lecturer  |
 | ----- | ------------------- | --------- |
-| 09.00-12.00 | Bring your own data | Åsa, Paulo |   
+| 09.00 | Bring your own data (until 12.00) | Åsa, Paulo |   
 
 <br/>
 
 <br/>
 
 Each day we will have cofee around 10.00 and at 15.00 during the exercises. Lunches will be at Svarta Räfven 12.15.
 
+<br/>
 
-* Icons are provided from www.svgrepo.com
+<div style="text-align: right; font-size: 5px"> Icons are provided from [www.svgrepo.com](www.svgrepo.com) </div>

travel.md

@@ -13,3 +13,7 @@ The main entrance is number 23a on [Karolinska Solna Campus Map](files/karta_cam
 The room Air & Fire is located on the ground floor to the left of the main entrance.
 
 To travel within Stockholm see [https://sl.se/en/](https://sl.se/en/).
+
+<br/>
+
+<div style="text-align: right; font-size: 5px"> Icons are provided from [www.svgrepo.com](www.svgrepo.com) </div>