From df1aeaac7aaff5fc33aa386418ea2ee46d0ced8d Mon Sep 17 00:00:00 2001 From: Hugo Tavares Date: Fri, 10 May 2024 10:56:05 +0100 Subject: [PATCH] update trainers --- index.md | 46 ++++++++++++++++++++++++---------------------- 1 file changed, 24 insertions(+), 22 deletions(-) diff --git a/index.md b/index.md index 6dc6450..c9030de 100644 --- a/index.md +++ b/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) + + [Practical](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/04_Preprocessing_And_QC.Exercise.html) - + [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)