update readme

Author: MelodyJIN-Y

README.md

@@ -34,7 +34,9 @@ No prior experience with single-cell analysis or Bioconductor is required. All c
 | R version | 4.3+ | 4.5.2 |
 | RStudio | 2023.06+ | Latest |
 
-## Workshop Outline (~3 hours)
+## Workshop Outline
+
+### Session 1: Core Single Cell Analysis (Morning, ~3 hours)
 
 | Module | Topic | Duration |
 |--------|-------|----------|
@@ -46,6 +48,10 @@ No prior experience with single-cell analysis or Bioconductor is required. All c
 | **Module 4** | Differential Expression | 55 min |
 | | Wrap-up & Q&A | 10 min |
 
+### Session 2: Downstream Analysis (Afternoon, ~3 hours)
+
+*Coming soon* - Additional downstream analyses using the same heart development dataset.
+
 ## Learning Objectives
 
 By the end of this workshop, participants will be able to:
@@ -77,92 +83,61 @@ The workshop uses snRNA-seq data from human heart tissue (Sim et al., 2021):
 | Analysis Step | Method | Package |
 |--------------|--------|---------|
 | Quality control | Per-cell metrics, filtering | Seurat |
-| Normalisation | SCTransform v2 | Seurat |
+| Normalisation | SCTransform v2 | Seurat, glmGamPoi |
 | Batch correction | Harmony | harmony |
 | Dimensionality reduction | PCA, UMAP | Seurat |
 | Clustering | Louvain algorithm | Seurat |
 | Cell type annotation | Marker-based (manual) | Seurat |
 | Differential expression | Pseudobulk + limma-voom | edgeR, limma |
 | Composition analysis | propeller | speckle |
 
-## Installation
+## Quick Start
+
+**Please complete setup at least one day before the workshop.**
+
+1. **Clone or download** this repository
+2. **Open** `single_cell_workshop.Rproj` in RStudio
+3. **Follow** [Module 0: Setup](https://phipsonlab.github.io/single_cell_workshop/articles/00_setup.html) for detailed instructions
+
+The setup involves:
+- Installing packages with `renv::restore()` (~10-15 minutes)
+- Downloading data from Zenodo (~420 MB, ~5 minutes)
 
-### Package Versions
+## Key Package Versions
 
-This workshop uses pinned package versions for reproducibility. The tutorial outputs were generated with these exact versions:
+This workshop uses pinned package versions for reproducibility:
 
 | Package | Version | Package | Version |
 |---------|---------|---------|---------|
 | R | 4.5.2 | Bioconductor | 3.22 |
 | Seurat | 5.4.0 | edgeR | 4.8.2 |
 | SeuratObject | 5.3.0 | limma | 3.66.0 |
 | harmony | 1.2.4 | speckle | 1.10.0 |
-| ggplot2 | 4.0.1 | | |
-
-### Step 1: Install Required Packages
-
-```r
-# Install remotes and BiocManager
-install.packages(c("remotes", "BiocManager"))
-
-# Set Bioconductor version
-BiocManager::install(version = "3.22", ask = FALSE)
-
-# Install Bioconductor packages
-BiocManager::install(c(
-    "edgeR",
-    "limma",
-    "org.Hs.eg.db",
-    "AnnotationDbi",
-    "speckle"
-))
-
-# Install CRAN packages with specific versions
-remotes::install_version("Seurat", version = "5.4.0")
-remotes::install_version("SeuratObject", version = "5.3.0")
-remotes::install_version("harmony", version = "1.2.4")
-remotes::install_version("ggplot2", version = "4.0.1")
-remotes::install_version("patchwork", version = "1.3.2")
-remotes::install_version("dplyr", version = "1.1.4")
-remotes::install_version("tidyr", version = "1.3.2")
-remotes::install_version("RColorBrewer", version = "1.1.3")
-remotes::install_version("clustree", version = "0.5.1")
-remotes::install_version("pheatmap", version = "1.0.13")
-```
-
-### Step 2: Download Workshop Data
-
-The workshop data (~420 MB) is hosted on Zenodo:
-
-```r
-# Download data from Zenodo
-zenodo_record <- "18237749"
-base_url <- paste0("https://zenodo.org/records/", zenodo_record, "/files/")
-
-dir.create("data", showWarnings = FALSE)
-for (f in c("heart-counts.Rds", "cellinfo_updated.Rds")) {
-    download.file(paste0(base_url, f, "?download=1"), file.path("data", f), mode = "wb")
-}
-```
-
-### Step 3: Verify Installation
-
-```r
-# Check that key packages load correctly
-packages <- c("Seurat", "harmony", "edgeR", "limma", "speckle")
-sapply(packages, requireNamespace, quietly = TRUE)
-```
+| glmGamPoi | 1.22.0 | | |
 
 ## Workshop Materials
 
+### Session 1: Core Single Cell Analysis
+
 | Module | Topic | Description |
 |--------|-------|-------------|
-| [Module 0](https://phipsonlab.github.io/single_cell_workshop/articles/00_setup.html) | Setup | Environment setup and package installation |
-| [Module 1](https://phipsonlab.github.io/single_cell_workshop/articles/01_quality_control.html) | Quality Control | QC metrics, doublet detection, cell filtering |
+| [Module 0](https://phipsonlab.github.io/single_cell_workshop/articles/00_setup.html) | Setup | Environment setup and data download |
+| [Module 1](https://phipsonlab.github.io/single_cell_workshop/articles/01_quality_control.html) | Quality Control | QC metrics, cell filtering |
 | [Module 2](https://phipsonlab.github.io/single_cell_workshop/articles/02_integration_clustering.html) | Integration | Normalisation, batch correction, clustering |
 | [Module 3](https://phipsonlab.github.io/single_cell_workshop/articles/03_cell_type_annotation.html) | Annotation | Marker genes and cell type assignment |
 | [Module 4](https://phipsonlab.github.io/single_cell_workshop/articles/04_differential_expression.html) | DE Analysis | Pseudobulk DE and composition analysis |
 
+### Session 2: Downstream Analysis
+
+*Coming soon* - Additional downstream analyses using the same heart development dataset.
+
+<!-- TODO: Add Session 2 modules here when ready
+| Module | Topic | Description |
+|--------|-------|-------------|
+| Module 5 | TBD | TBD |
+| Module 6 | TBD | TBD |
+-->
+
 ## Citation
 
 If you use materials from this workshop, please cite:

_pkgdown.yml

@@ -11,7 +11,7 @@ home:
     using human heart development snRNA-seq data.
   strip_header: true
   sidebar:
-    structure: [links, license, authors]
+    structure: [links, license]
   links:
     - text: Original analysis workflow
       href: https://bphipson.github.io/Human_Development_snRNAseq/