From b53c5f2e88f10c3322aec575e19adaf2ae891c3f Mon Sep 17 00:00:00 2001 From: AbbiEdwards Date: Mon, 11 Nov 2024 12:39:23 +0000 Subject: [PATCH] updating index --- index.md | 47 +++++++++++++++++++++++------------------------ 1 file changed, 23 insertions(+), 24 deletions(-) diff --git a/index.md b/index.md index b11d1c5..e4521d2 100644 --- 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) + -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) + 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)) + -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)) @@ -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 @@ -93,15 +92,15 @@ 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) -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) @@ -109,7 +108,7 @@ differential expression analysis of RNA-seq data. 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)