This page provides links to documentation, tutorials, and publications for the tools and methods used in this workshop.
Session 1: Single-Cell RNA-seq Fundamentals
Data Processing & Visualisation
| Tool | Description | Links |
|---|---|---|
| Seurat | Comprehensive R toolkit for single-cell analysis | Website · Vignettes · GitHub |
| Harmony | Fast integration of single-cell data | GitHub · Paper |
Differential Expression
| Tool | Description | Links |
|---|---|---|
| edgeR | Differential expression analysis of count data | Bioconductor · User Guide · Paper |
| limma | Linear models for microarray and RNA-seq | Bioconductor · User Guide · Paper |
| voom | Precision weights for RNA-seq | Paper |
Composition Analysis
| Tool | Description | Links |
|---|---|---|
| speckle/propeller | Cell type proportion testing | Bioconductor · Vignette · Paper |
Session 2: [Afternoon Session]
Links to be added
| Tool | Description | Links |
|---|---|---|
| [Tool 1] | [Description] | [Links] |
| [Tool 2] | [Description] | [Links] |
| [Tool 3] | [Description] | [Links] |
General Resources
Bioconductor
| Resource | Description |
|---|---|
| Bioconductor | Open source software for bioinformatics |
| Support Forum | Community Q&A for Bioconductor packages |
| Workflows | End-to-end analysis workflows |
Single-Cell Analysis
| Resource | Description |
|---|---|
| OSCA Book | Orchestrating Single-Cell Analysis with Bioconductor |
| Single Cell Best Practices | Community best practices for scRNA-seq |
| scRNA-tools | Database of single-cell analysis tools |
Statistics & Methods
| Resource | Description |
|---|---|
| StatQuest | Statistics explained visually |
| Modern Statistics for Modern Biology | Free online textbook |
Original Study
This workshop uses data from:
Sim CB, Phipson B, Ziemann M, et al. Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor. Circulation. 2021;143(10):1614-1628.
| Resource | Link |
|---|---|
| Paper | doi:10.1161/CIRCULATIONAHA.120.051921 |
| Analysis workflow | bphipson.github.io/Human_Development_snRNAseq |
| GEO Data | GSE161921 |
| Workshop Data (Zenodo) | zenodo.org/records/18237749 |