updating index

bioinformatics-core-shared-training · Nov 11, 2024 · b53c5f2 · b53c5f2
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diff --git a/index.md b/index.md
@@ -1,5 +1,5 @@
 # Introduction to Bulk RNA-seq data analysis
-### 2nd, 3rd, 4th Oct 2024
+### 12, 19, 26 Nov 2024
 #### In person
 #### Bioinformatics Training Facility, Craik-Marshall Building, Downing Site, University of Cambridge
 
@@ -8,11 +8,10 @@
 ## Instructors
 
 * Ashley Sawle (CRUK Cambridge Institute)
-* Abbi Edwards (CRUK Cambridge Institute)
 * Betty Wang (Dpt Clinical Neurosciences, University of Cambridge)
-* Ian Tsang (NIAB)
-* Jiayin Hong (Dpt Biochemistry, University of Cambridge)
-* Ramy Ragheb (Stem Cell Institute, University of Cambridge)
+* Chandra Chilamakuri (CRUK Cambridge Institute)
+* Yuki Ye (Dpt Clinical Neurosciences, University of Cambridge)
+* Erin Doody (Sainsbury Laboratory)
 
 ## Outline
 
@@ -40,30 +39,30 @@ differential expression analysis of RNA-seq data.
 
 ### Day 1
 
-**Trainers:** Abbi, Betty, Ian, Ramy, Hugo
+**Trainers:** 
 
 9:30 - 9:45 - [Welcome](https://docs.google.com/presentation/d/13mwQfPCpYzj0iz5EyTQHXRd1KNwfds2ILdY8EiK2020/edit?usp=sharing)! - Bajuna
 
-9:45 - 10:15 - [Introduction to RNAseq Methods](Bulk_RNAseq_Course_Base/Markdowns/01_Introduction_to_RNAseq_Methods.html) - Betty
+9:45 - 10:15 - [Introduction to RNAseq Methods](Bulk_RNAseq_Course_Base/Markdowns/01_Introduction_to_RNAseq_Methods.html) - Chandra
 
-10:15 - 11:00 [Raw read file format and QC](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_introduction.html) - Betty
+10:15 - 11:00 [Raw read file format and QC](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_introduction.html) - Erin
 
   - [Practical](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_practical.html)
-  - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_solutions.html)
+  <!-- - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_solutions.html) -->
 
-11:00 - 13:30 [Alignment and Quantification of Gene Expression with Salmon](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_introduction.html) - Hugo
+11:00 - 13:30 [Alignment and Quantification of Gene Expression with Salmon](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_introduction.html) - Erin
 
   - [Practical](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_practical.html)  
-  - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_solutions.html)
+ <!-- - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_solutions.html) -->
 
 13:30 - 14:30 Lunch
 
-14:30 - 15:30 [QC of alignment](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_introduction.html) - Abbi
+14:30 - 15:30 [QC of alignment](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_introduction.html) - Ash
 
   - [Practical](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_practical.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_practical.pdf))  
-   - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_solutions.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_solutions.pdf))
+   <!-- - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_solutions.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_solutions.pdf)) -->
 
-15.30 - 17.30 [Data Exploration in R](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration_Slides.html) - Ian
+15.30 - 17.30 [Data Exploration in R](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration_Slides.html) - Ash
 
   - [Practical](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.pdf))
   <!-- - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration_solutions.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration_solutions.pdf)) -->
@@ -72,15 +71,15 @@ differential expression analysis of RNA-seq data.
 
 ### Day 2
 
-**Trainers:** Ash, Abbi (AM), Ian, Ramy
+**Trainers:** 
 
-9:30 - 10:15  [Introduction to RNAseq Analysis in R](Bulk_RNAseq_Course_Base/Markdowns/06_Introduction_to_RNAseq_Analysis_in_R.html) - Abbi
+9:30 - 10:15  [Introduction to RNAseq Analysis in R](Bulk_RNAseq_Course_Base/Markdowns/06_Introduction_to_RNAseq_Analysis_in_R.html) - Betty
 
-10:15 - 11:30 [Statistical Analysis of Bulk RNAseq Data](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/07_Statistics_1.pdf) - Abbi
+10:15 - 11:30 [Statistical Analysis of Bulk RNAseq Data](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/07_Statistics_1.pdf) - Betty
 
-11:30 - 17:30 [Linear Models in R and DESeq2 (Slides)](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/07_Statistics_2.pdf) - Abbi/Ash
+11:30 - 17:30 [Linear Models in R and DESeq2 (Slides)](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/07_Statistics_2.pdf) - Chandra
 
-  - [Practical - Differential Expression for RNA-seq](Bulk_RNAseq_Course_Base/Markdowns/08_DE_analysis_with_DESeq2.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/08_DE_analysis_with_DESeq2.pdf)) - Ash/Abbi
+  - [Practical - Differential Expression for RNA-seq](Bulk_RNAseq_Course_Base/Markdowns/08_DE_analysis_with_DESeq2.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/08_DE_analysis_with_DESeq2.pdf)) - Chandra
   <!-- - [practical solutions](Bulk_RNAseq_Course_Base/Markdowns/08_DE_analysis_with_DESeq2_solutions.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/08_DE_analysis_with_DESeq2_solutions.pdf)) -->
   <!-- - [live script](live_scripts/DESeq2_script.R)  -->
 
@@ -93,23 +92,23 @@ differential expression analysis of RNA-seq data.
 
 ### Day 3
 
-**Trainers:** Ash, Ian, Jiayin, Ramy
+**Trainers:** 
 
-9:30 - 9:45 - [Recap of Day 1 and 2](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/Analysis_of_RNA-seq_data_day3recap.pdf) - Ash
+9:30 - 9:45 - [Recap of Day 1 and 2](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/Analysis_of_RNA-seq_data_day3recap.pdf) - Chandra
 
-9:45 - 11:00 [Annotation of RNA-seq results](Bulk_RNAseq_Course_Base/Markdowns/09_Annotation_Slides.html) - Ash. 
+9:45 - 11:00 [Annotation of RNA-seq results](Bulk_RNAseq_Course_Base/Markdowns/09_Annotation_Slides.html) - Puspendu
   - [Practical](Bulk_RNAseq_Course_Base/Markdowns/09_Annotation.html)
   <!-- - [live script](live_scripts/visualisation.R) -->
 
-11:00 - 12.30 [Visualisation differential expression results](Bulk_RNAseq_Course_Base/Markdowns/10_Data_Visualisation_Slides.html) - Jiayin
+11:00 - 12.30 [Visualisation differential expression results](Bulk_RNAseq_Course_Base/Markdowns/10_Data_Visualisation_Slides.html) - Yuki
 
    - [Practical](Bulk_RNAseq_Course_Base/Markdowns/10_Data_Visualisation.html)
   <!-- - [practical solutions](Bulk_RNAseq_Course_Base/Markdowns/10_Data_Visualisation_solutions.html) -->
   <!-- - [live script](live_scripts/visualisation.R) -->
 
 12.30 - 13.30 Lunch
 
-13.30 - 16:30  [Gene-set testing](Bulk_RNAseq_Course_Base/Markdowns/11_Gene_set_testing_introduction.html) - Ian
+13.30 - 16:30  [Gene-set testing](Bulk_RNAseq_Course_Base/Markdowns/11_Gene_set_testing_introduction.html) - Puspendu
    - [Practical (html)](Bulk_RNAseq_Course_Base/Markdowns/11_Gene_set_testing.html) [(pdf)](Bulk_RNAseq_Course_Base/Markdowns/11_Gene_set_testing.pdf)
   <!-- - [Practical solutions (html)](Bulk_RNAseq_Course_Base/Markdowns/11_Gene_set_testing_solutions.html) (pdf)](Bulk_RNAseq_Course_Base/Markdowns/11_Gene_set_testing_solutions.pdf) -->
   <!-- - [Live Script](live_scripts/gene_set_testing.R) -->