From 3de10fbe46ce71eff8c015ec587068d9af89c952 Mon Sep 17 00:00:00 2001 From: Hugo Tavares Date: Mon, 11 Mar 2024 13:23:15 +0000 Subject: [PATCH] update trainers --- index.md | 123 +++++++++++++++++++------------------------------------ 1 file changed, 43 insertions(+), 80 deletions(-) diff --git a/index.md b/index.md index e705b79..ea17485 100644 --- a/index.md +++ b/index.md @@ -1,17 +1,17 @@ # Introduction to Bulk RNA-seq data analysis -### 17th, 24th Nov and 1st Dec -#### Online +### 15, 18, 19 March 2024 +#### In person #### Bioinformatics Training Facility, Craik-Marshall Building, Downing Site, University of Cambridge ![](Bulk_RNAseq_Course_Base/images/CRUK_Cambridge_Major_Centre_logo.jpg) ## Instructors -* Abigail Edwards - Bioinformatics Core, Cancer Research UK Cambridge Institute -* Adam Reid - Gurdon Institute, University of Cambridge -* Tom Smith - MRC Toxicology, University of Cambridge -* Ulrika Yuan - Department of Biochemistry, University of Cambridge -* Zac Scurlock - Department of Pathology, University of Cambridge +* Ash Sawle - Bioinformatics Core, Cancer Research UK Cambridge Institute +* Chandra Chilamakuri - Bioinformatics Core, Cancer Research UK Cambridge Institute +* Erin Doody - Sainsbury Laboratory, University of Cambridge +* Ian Tsang - NIAB, Cambridge +* Puspendu Sardar - Department of Medicine, University of Cambridge ## Outline @@ -33,127 +33,90 @@ be aware that timings for different sections laid out in the schedule below may not be adhered to. There may be some necessity to make adjustments to the course as we go. -> ## Prerequisites -> -> __**Some basic experience of using a UNIX/LINUX command line is assumed**__ -> -> __**Some R knowledge is assumed and essential. Without it, you will struggle on this course.**__ -> If you are not familiar with the R statistical programming language we -> strongly encourage you to work through an introductory R course before -> attempting these materials. -> We recommend our [Introduction to R course](https://bioinformatics-core-shared-training.github.io/r-intro/) +## Prerequisites -## Shared Google Document +* __**Basic experience of using a UNIX/LINUX command line is assumed**__ + * Watch this [overview video](https://drive.google.com/file/d/1qo_eNXaYSphU_Xpk0jzDHp1wJzyfSwAT/view?usp=drive_link) (and [accompanying materials](https://cambiotraining.github.io/unix-shell/) up to section 6). -This [Google Document](https://docs.google.com/document/d/1nqnelPJFx_Gvw8Mz83AEzcP2cII2ZlLpMlRDBEdWFeU/edit?usp=sharing) contains useful information and links. - -Please use it to post any long form questions you have during the course. - -The trainers will be monitoring the document and will answer questions as quickly as they can. - -## Introduce Yourself - -There is another Google Doc [Google Document](https://docs.google.com/document/d/19xeAvseME9N7x0NE8hMOm3MUCHxKg0IiHhSQuc0fBDE/edit?usp=drive_link). -Please write a couple sentences here to introduce yourself to the class, tell us a bit about your background and what you hope to get out of this course. -If you are a student or staff at the University of Cambridge, tell us which Department you are in. - -## Course etiquette - -As this course is being taught online and there are a large number of participants, -we will all need to follow a [few simple rules](https://docs.google.com/presentation/d/e/2PACX-1vQv9nTlsdRC9iZJU138tLL1jrwNoryp8P-FnXxb_ugOOWjbav4QHTLYLLZj2KK4kTO0_3x3VlzSdrUu/pub?start=false&loop=false&delayms=3000) to ensure things run as smoothly as possible: - -1. Please mute your microphone - -2. To get help from a tutor, please click the "Raise Hand" button in Zoom: - - ![](Bulk_RNAseq_Course_Base/images/raise_hand.png) - - This can be found by clicking on the 'Participants' button. A tutor will - then contact you in the chat. If necessary, you and the tutor can be moved - to a breakout room where you can discuss your issue in more detail. - -3. Please ask any general question by typing it into the Google Doc mentioned above - -4. During practicals, when you are done, please press the green "Yes" button: - - ![](Bulk_RNAseq_Course_Base/images/yes_button.png) - - This way we will know when we can move on. +* __**Some R knowledge is assumed and essential. Without it, you will struggle on this course.**__ + * If you are not familiar with the R statistical programming language we strongly encourage you to work through an introductory R course before attempting these materials. + * We recommend our [Introduction to R course](https://bioinformatics-core-shared-training.github.io/r-intro/) ## Timetable ### Day 1 -**Trainers:** Abbi, Adam, Ulrika, Tom, Zac +**Trainers:** Ash, Chandra, Erin, Ian, Puspendu -9:30 - 9:45 - [Welcome](https://docs.google.com/presentation/d/1u-UFD5LzBh0FTV54e-TCJJOrCRtdWxM000rQw-a5w6w/edit?usp=sharing)! +9:30 - 9:45 - [Welcome](https://docs.google.com/presentation/d/1u-UFD5LzBh0FTV54e-TCJJOrCRtdWxM000rQw-a5w6w/edit?usp=sharing)! -9:45 - 10:15 - [Introduction to RNAseq Methods](Bulk_RNAseq_Course_Base/Markdowns/01_Introduction_to_RNAseq_Methods.html) - Tom +9:45 - 10:15 - [Introduction to RNAseq Methods](Bulk_RNAseq_Course_Base/Markdowns/01_Introduction_to_RNAseq_Methods.html) - Erin -10:15 - 11:00 [Raw read file format and QC](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_introduction.html) - Adam +10:15 - 11:00 [Raw read file format and QC](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_introduction.html) - Ian - [Practical](Bulk_RNAseq_Course_Base/Markdowns/02_FastQC_practical.html) - + -11:00 - 13:30 [Alignment and Quantification of Gene Expression with Salmon](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_introduction.html) - Adam +11:00 - 13:30 [Alignment and Quantification of Gene Expression with Salmon](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_introduction.html) - Chandra - [Practical](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_practical.html) - - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/03_Quantification_with_Salmon_practical.Solutions.html) + 13:30 - 14:30 Lunch -14:30 - 15:30 [QC of alignment](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_introduction.html) - Ulrika +14:30 - 15:30 [QC of alignment](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_introduction.html) - Chandra - [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_practical.Solutions.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/04_Quality_Control_practical.Solutions.pdf)) + -15.30 - 17.30 [Data Exploration in R](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.pdf)) - Abbi +15.30 - 17.30 [Data Exploration in R](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.pdf)) - Ash - - [Practical solutions](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.Solutions.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/05_Data_Exploration.Solutions.pdf)) - - [Live Script](live_scripts/data_exploration.R) + + ### Day 2 -**Trainers:** Abbi, Adam, Raquel, Tom +**Trainers:** Ash, Chandra, Erin, Ian, Puspendu -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) - Ash -10:15 - 13:00 Statistical Analysis of Bulk RNAseq Data +10:15 - 13:00 Statistical Analysis of Bulk RNAseq Data - Ash - - Part I: [Statistics of RNA-seq analysis](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/RNA-seq_stats.pdf) - Abbi - - Part II: [Linear Models in R and DESeq2](Bulk_RNAseq_Course_Base/Markdowns/07_Linear_Models.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/07_Linear_Models.pdf)) - Abbi + - Part I: [Statistics of RNA-seq analysis](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/RNA-seq_stats.pdf) + - Part II: [Linear Models in R and DESeq2](Bulk_RNAseq_Course_Base/Markdowns/07_Linear_Models.html) ([pdf](Bulk_RNAseq_Course_Base/Markdowns/07_Linear_Models.pdf)) - [Slides](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/Statistical_models_in_R_DESeq2.pdf) - Find the worksheet in `Course_Materials/stats/models_in_r_worksheet.R` 13:00 - 14:00 Lunch -14:00 - 17:30 - [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)) - Adam - - [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/deseq_day2_afternoon.R) --> +14:00 - 17:30 - [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 + + - [DESeq2 results extraction cheatsheet](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/DESeq2_results_cheatsheet.pdf) - [extra models plots](Bulk_RNAseq_Course_Base/additional_scripts_and_materials/Expl_all.pdf) ### Day 3 -**Trainers:** Abbi, Adam, Ulrika, Raquel +**Trainers:** Ash, Chandra, Erin, Ian, Puspendu -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) - Abbi +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 - 12.30 [Annotation and Visualisation of RNA-seq results](Bulk_RNAseq_Course_Base/Markdowns/09_Annotation_and_Visualisation.html) - Ulrika - - [practical solutions](Bulk_RNAseq_Course_Base/Markdowns/09_Annotation_and_Visualisation_Solutions.html) - - [live script](live_scripts/Live_script_Ulrika.R) +9.45 - 12.30 [Annotation and Visualisation of RNA-seq results](Bulk_RNAseq_Course_Base/Markdowns/09_Annotation_and_Visualisation.html) - Ian / Chandra + + 12.30 - 13.30 Lunch -13.30 - 16:30 [Gene-set testing](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing_introduction.html) - Abbi +13.30 - 16:30 [Gene-set testing](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing_introduction.html) - Ash + - [Practical (html)](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing.html) [(rmd)](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing.Rmd) [(pdf)](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing.pdf) - - [Practical solutions (html)](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing.Solutions.html) [(rmd)](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing.Solutions.Rmd) [(pdf)](Bulk_RNAseq_Course_Base/Markdowns/10_Gene_set_testing.Solutions.pdf) - - [Live Script](live_scripts/GeneSetTesting.R) + + - + ## Data, software and materials