Revise workshop schedule and instructor list

Updated workshop dates, instructors, and session details.

Author: tavareshugo

index.md

@@ -1,17 +1,16 @@
 # Introduction to single-cell RNA-seq data analysis
 
-### 12th, 19th, 26th February 2025 || 09:30 - 17:00
-#### Online via Zoom
+### 1st, 2nd, 3rd October 2025 || 09:30 - 17:00
+#### In-person at the Craik Marshall training room ([map](https://maps.app.goo.gl/wJLCDC7XU67vUrEF7))
 
 ![](UnivCambridge_ScRnaSeqIntro_Base/Images/uniOfCamCrukLogos.png)
 
 ## Instructors
 
-- Abbi Edwards (CRUK)
-- Betty Wang (Clinical Neurosciences)
+- Adam Reid (Gurdon Institute)
 - Chandra Chilamakuri (CRUK)
-- Jiayin Hong (Sanger Institute)
-- Erin Doody (Sainsbury Laboratory)
+- Hugo Tavares (Bioinformatics Training)
+- Ramy Ragheb (Exeter University)
 - Guest Speaker: Kasia Kania (Cosyne Therapeutics)
 
 ## Outline
@@ -54,18 +53,17 @@ of gene expression data, such as TSNE, UMAP and violin plots.
 
 ### Day 1
 
-
 * 09:30 - 09:45 **Welcome** - Hugo
 * 09:45 - 10:30 **Introduction to Single Cell Technologies** - Katarzyna Kania
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/01_Introduction.pdf)
-* 10:30 - 10:44 **Preamble**: data set and workflow - Chandra
+* 10:30 - 10:44 **Preamble**: data set and workflow - Adam
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/02_PreambleSlides.html)
 * 10:45 - 11:00 - **Break**
-* 11:00 - 12:30 Library structure, **cellranger** for alignment and cell calling - Chandra
+* 11:00 - 12:30 Library structure, **cellranger** for alignment and cell calling - Adam
     + [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** - Erin
+* 13:30 - 17:00 **QC and exploratory analysis** - Ramy
     + [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) -->
@@ -74,62 +72,91 @@ of gene expression data, such as TSNE, UMAP and violin plots.
 
 ### Day 2
 
-
 * 09:30 - 09:40 **Recap** - Chandra
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/00_Day1_Recap.html)
 * 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
+* 13:30 - 15:25 **Feature selection and dimensionality reduction** - Ramy
     + [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**
-* 15:35 - 17:30 **Batch correction and data set integration** - Abbi
+* 15:35 - 17:30 **Batch correction and data set integration** - Hugo
     + [Slides](UnivCambridge_ScRnaSeqIntro_Base/Slides/07_DataIntegrationAndBatchCorrectionSlides.html) \([pdf](UnivCambridge_ScRnaSeqIntro_Base/Slides/07_DataIntegrationAndBatchCorrectionSlides.pdf)\)
     + [Demonstration](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/07_Dataset_Integration.html)
 
 ### Day 3
 
-* 09:30 - 09:40 Recap - Abbi
-* 09:40 - 11:05 **Cell clustering** - Abbi
+* 09:30 - 09:40 Recap - Hugo
+* 09:40 - 11:05 **Cell clustering** - 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** - Betty
+* 11:15 - 12:30 **Identification of cluster marker genes** - Ramy
     + [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** - Chandra (DE) & Abbi (DA)
+* 13:30 - 17:00 **Differential Expression and Abundance Analysis** - Adam (DE) & Hugo (DA)
     + [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)
 
-
-## Extended Materials
-
-* **Seurat** walkthrough:
-  * Part 1: [Data pre-processing](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/101-seurat_part1.html)
-  * Part 2: [Cell clustering and annotation](UnivCambridge_ScRnaSeqIntro_Base/Markdowns/101-seurat_part2.html)
-
-
 ## Software Installation
 
 You can make use of the computer environment provided for the course, which is ready for use and have the necessary data & software installed.
 However, if you want to run the analysis on your own computer, you can follow these instructions.
 
+### R and Bioconductor packages
+
 * Download and install R: https://cloud.r-project.org/
   * (Windows users only): Download and install RTools: https://cran.r-project.org/bin/windows/Rtools/
 * Download and install RStudio: https://www.rstudio.com/products/rstudio/download/#download
 * Open RStudio and run the following commands from the console:
+
     ```r
     install.packages("BiocManager")
-    BiocManager::install(c("AnnotationHub", "BiocParallel", "BiocSingular", "DropletUtils", "PCAtools", "batchelor", "bluster", "cluster", "clustree", "dynamicTreeCut", "edgeR", "ensembldb", "ggplot2", "igraph", "patchwork", "pheatmap", "scater", "scran", "tidyverse"))
+    BiocManager::install(c("AnnotationHub", "BiocParallel", "BiocSingular", 
+                           "DropletUtils", "PCAtools", "batchelor", "miloR",
+                           "bluster", "cluster", "clustree", "dynamicTreeCut", 
+                           "edgeR", "ensembldb", "ggplot2", "igraph", 
+                           "patchwork", "pheatmap", "scater", "scran", "tidyverse"))
     ```
 
+### Cellranger
+
 For Cellranger, you will need to use a Linux machine.
-See the [installation instructions from 10x Genomics](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation).
+The instructions below are based on the [installation instructions from 10x Genomics](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation).
+
+1. Create a directory for your software. In this example, we will use `$HOME/software`:
+
+    ```bash
+    mkdir -p $HOME/software
+    cd $HOME/software
+    ```
+
+2. Download cellranger from [10xgenomics](https://www.10xgenomics.com/support/software/cell-ranger/downloads).
+  You will need to register with 10x, and they will then provide you with a link to download a `.tar.gz` archive file.
+  You can use `wget` to download the file:
+
+    ```bash 
+    wget -O cellranger-9.0.0.tar.gz "YOUR-LINK-HERE"
+    ```
+
+1. Unpack the downloaded file:
+
+    ```bash
+    tar -xzvf cellranger-9.0.0.tar.gz
+    ```
+
+2. Add the Cellranger directory to your `$PATH`, allowing you to use the `cellranger` command from any location: 
+
+    ```bash
+    export PATH=$HOME/software/cellranger-9.0.0:$PATH
+    ```
+
+	***You may want to add this command to your `$HOME/.bashrc` for convenience.***
 
 
 ## Acknowledgments:
@@ -140,6 +167,6 @@ and the [Hemberg Group course materials](https://www.singlecellcourse.org/). Add
 
 The materials have been contributed to by many individuals over the last 2 years, including:
 
-Abigail Edwards, Ashley D Sawle, Chandra Chilamakuri, Kamal Kishore, Stephane Ballereau, Zeynep Kalendar Atak, Hugo Tavares, Jon Price, Katarzyna Kania, Roderik Kortlever, Adam Reid, Tom Smith
+Abigail Edwards, Ashley D Sawle, Chandra Chilamakuri, Kamal Kishore, Stephane Ballereau, Zeynep Kalendar Atak, Hugo Tavares, Jon Price, Katarzyna Kania, Roderik Kortlever, Adam Reid, Tom Smith, Jiawei Wang
 
 Apologies if we have missed anyone!