update trainers

index.md

@@ -1,18 +1,20 @@
 # Introduction to single-cell RNA-seq data analysis
 
-### 16, 17, 20 Feb || 09:30 - 17:30
-### Bioinformatics Training Facility, Craik-Marshall Building, Downing Site, University of Cambridge
+### 16th, 17th and 20th May 2024 || 09:30 - 17:30
+#### In-person at the Craik Marshall training room ([map](https://maps.app.goo.gl/wJLCDC7XU67vUrEF7))
 
 ![](UnivCambridge_ScRnaSeqIntro_Base/Images/uniOfCamCrukLogos.png)
 
 ## Instructors
 
-* Abigail Edwards - Bioinformatics Core, Cancer Research UK Cambridge Institute
+* **Invited speaker:** Katarzyna Kania - CoSyne Therapeutics
+
 * Adam Reid - Bioinformatics Core, Gurdon Institute
+* Ash Sawle - Bioinformatics Core, Cancer Research UK Cambridge Institute
+* Betty Wang - Department Clinical Neurosciences
+* Chandra Chilamakuri - Bioinformatics Core, Cancer Research UK Cambridge Institute
+* Hugo Tavares - Bioinformatics Training Facility, Cambridge
 * Jiawei Wang - EBI
-* Jiayin Hong - Department of Biochemistry
-* Jon Price - Biochemistry Department, University of Cambridge
-* Katarzyna Kania - Genomics Core, Cancer Research UK Cambridge Institute
 
 
 ## Outline
@@ -45,7 +47,7 @@ of gene expression data, such as TSNE, UMAP and violin plots.
   relating to pediatric leukemia, with four sample types, including:
   * pediatric Bone Marrow Mononuclear Cells (PBMMCs)
   * three tumour types: ETV6-RUNX1, HHD, PRE-T  
-* The data used in the course can be [downloaded from Dropbox](https://www.dropbox.com/sh/qwxgat50tsg8m3r/AAAzQd5WXuEBGOFl3m4f5B1La?dl=1) (the file is 4.2GB compressed and XXGB when uncompressed, so make sure you have enough space on your computer). Please note that:
+* The data used in the course can be [downloaded from Dropbox](https://www.dropbox.com/scl/fo/9uu4iuapr60jfu2bvggdz/h?rlkey=64vrtse3lm8eb3zu9ovlxdp1a&st=t9e1bm9x&dl=0). Please note that:
   * these data have been processed for teaching purposes and are therefore not suitable for research use;
   * all the data is provided on our training machines, you don't need to download it to attend the course.
 
@@ -55,37 +57,37 @@ of gene expression data, such as TSNE, UMAP and violin plots.
 
 ### Day 1
 
-Trainers: Abbi, Adam, Jiayin, Jon
+Trainers: Adam, Chandra, Jiawei
 
-* 09:30 - 09:40 **Welcome** - Abbi
+* 09:30 - 09:40 **Welcome** - Hugo
 * 09:40 - 10:25 **Introduction to Single Cell Technologies** - Katarzyna Kania
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/01_Introduction.pdf)
 * 10:25 - 10:30 - **Break**
-* 10:30 - 10:40 **Preamble**: data set and workflow - Jon
+* 10:30 - 10:40 **Preamble**: data set and workflow - Chandra
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/02_PreambleSlides.html)
-* 10:40 - 12:30 Library structure, **cellranger** for alignment and cell calling - Jon
+* 10:40 - 12:30 Library structure, **cellranger** for alignment and cell calling - Chandra
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/03_CellRangerSlides.html) \([pdf](UnivCambridge_ScRnaSeqIntro_Base/Slides/03_CellRangerSlides.pdf)\)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/03_CellRanger.html)
 * 12:30 - 13:30 **Lunch break**
 * 13:30 - 17:00 **QC and exploratory analysis** - Adam
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/04_QualityControlSlides.html) \([pdf](UnivCambridge_ScRnaSeqIntro_Base/Slides/04_QualityControlSlides.pdf)\)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/04_Preprocessing_And_QC.html)
-        + [Demo live script](live_scripts/04_demonstration_live_script.R)
+        <!-- + [Demo live script](live_scripts/04_demonstration_live_script.R) -->
     + [Practical](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/04_Preprocessing_And_QC.Exercise.html)  
-        + [Exercise live script](live_scripts/04_exercise_live_script.R)
+        <!-- + [Exercise live script](live_scripts/04_exercise_live_script.R) -->
 
 ### Day 2
 
-Trainers: Adam, Jiawei, Jiayin, Jon
+Trainers: Adam, Chandra, Hugo
 
-* 09:30 - 09:40 **Recap** - Jon
+* 09:30 - 09:40 **Recap** - Chandra
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/00_Day1_Recap.html)
-* 09:40 - 12:30 **Normalisation** - Jon
+* 09:40 - 12:30 **Normalisation** - Chandra
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/05_NormalisationSlides.html) \([pdf](UnivCambridge_ScRnaSeqIntro_Base/Slides/05_NormalisationSlides.pdf)\)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/05_Normalisation.html)    
     + [Practical](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/05_Normalisation_exercises.html)
 * 12:30 - 13:30 **lunch break**
-* 13:30 - 15:25 **Feature selection and dimensionality reduction** - Jiayin / Hugo
+* 13:30 - 15:25 **Feature selection and dimensionality reduction** - Hugo
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/06_FeatureSelectionAndDimensionalityReduction_slides.html) \([pdf](UnivCambridge_ScRnaSeqIntro_Base/Slides/06_FeatureSelectionAndDimensionalityReduction_slides.pdf)\)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/06_FeatureSelectionAndDimensionalityReduction.html)
 * 15:25 - 15:35 10 min **break**
@@ -95,18 +97,18 @@ Trainers: Adam, Jiawei, Jiayin, Jon
 
 ### Day 3
 
-Trainers: Abbi, Adam, Jiawei, Jiayin
+Trainers: Ash, Betty, Hugo, Jiawei
 
-* 09:30 - 09:40 Recap - Adam
-* 09:40 - 11:05 **Clustering** - Adam
+* 09:30 - 09:40 Recap - Hugo
+* 09:40 - 11:05 **Clustering** - Jiawei / Hugo
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/08_ClusteringSlides.html)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/08_Clustering.html)
 * 11:05 - 11:15 10 min **break**
-* 11:15 - 12:30 **Identification of cluster marker genes** - Abbi
+* 11:15 - 12:30 **Identification of cluster marker genes** - Jiawei / Hugo
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/09_ClusterMarkerGenes.html)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/09_Cluster_Marker_Genes.html)
 * 12:30 - 13:30 **lunch break**
-* 13:30 - 17.30 **Differential Expression and Abundance Analysis** - Abbi
+* 13:30 - 17.30 **Differential Expression and Abundance Analysis** - Ash
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/10_DifferentialExpressionAndAbundance.pdf) 
     + [Demonstration - Differential Expression](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/10_Differential_Expression.html)
     + [Demonstration - Differential Abundance](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/11_Differential_Abundance.html)