Additional resources and materials

Introduction

This whole course was aimed on beginners in the single-cell RNA-seq analysis word. While our practical sessions begin with Seurat due to its accessibility, we emphasize transitioning to Bioconductor-based workflows using the SingleCellExperiment class for reproducibility and interoperability.

We outline four essential resources: - OSCA (Orchestrating Single-Cell Analysis) – the primary conceptual and technical reference for Bioconductor workflows. - Bioconductor ecosystem – the underlying structure for reproducible and transparent data analysis. - scdrake – our automated, OSCA-inspired end‑to‑end workflow created in our lab. - MetaCentrum – national (Czech republic) HPC infrastructure for students and researchers in the Czech Republic who need computational resources.

OSCA: Orchestrating Single-Cell Analysis with Bioconductor

OSCA is a comprehensive online book introducing single-cell analysis principles and their implementation using Bioconductor tools. It provide solid foundation of tools for scRNA-seq analysis (in the Bioconductor environment), together explanation of used tools and suggested workflows/code snipets. the steps of a simple single-cell RNA-seq analysis, involving quality control, normalization, various forms of dimensionality reduction, clustering into subpopulations, detection of marker genes, and annotation of cell types. It is intended for users who already have some familiarity with R and want to get hands-on with some basic single-cell analyses

Bioconductor and SingleCellExperiment

The Bioconductor ecosystem offers modular, transparent, and well‑tested tools for scRNA-seq.

SingleCellExperiment (SCE)

The SingleCellExperiment class serves as a unified container for storing: - count matrices - metadata (cell, gene, sample) - dimensionality reduction results - alternative assays (e.g., logcounts, corrected data)

Benefits

  • Clear structure for all analysis outputs
  • Seamless interoperability with dozens of Bioconductor packages
  • Makes it easy to track every transformation applied to the data

Key Packages

scater

  • Quality control
  • Visualization
  • Basic preprocessing

scran

  • Normalization
  • Variance modelling
  • Clustering support functions

batchelor

  • Batch correction (fastMNN, rescaling)

Why we encourage switching to Bioconductor

  • Transparent methodology
  • Robust documentation
  • Long-term reproducibility
  • Better suited for HPC environments and scripted analyses
  • Better control over analysis

scdrake: Our OSCA-Inspired Pipeline

scdrake is our reproducible workflow for scRNA-seq preprocessing and analysis.

Key features

  • Scalable, reproducible, reducing manual coding errors, extendable
  • Ideal for droplet-based technologies
  • Automated workflows, configurable using yaml config files
  • Based of OSCA best practices
  • Automatic HTML reporting with rich graphical outpus based on customiyable RMarkdwon documents
  • Full reproducibility using {drake} and containerized environments as {Docker}
  • Suitable for spot-based spatial transcriptomics data using spatial extension

MetaCentrum

MetaCentrum is the Czech Republic’s national grid infrastructure, providing researchers, scientists, and students with access to powerful computing resources for solving demanding computational tasks. As part of CESNET and the national e-infrastructure e-INFRA CZ, MetaCentrum connects an extensive network of distributed computing and storage capacities across universities and research institutions.

OnDemand

Open OnDemand is a service that allows users to access computing resources via a web browser in graphical mode. Users can run standard PBS jobs, access frontend terminals, copy files between our storage repositories, or run several graphical applications in their browser. The most commonly used applications available include Matlab, RStudio, Jupyter Lab/Notebook ANSYS, MetaCentrum Remote Desktop, and VMD (see the complete list of GUI applications available through OnDemand). Graphical sessions are persistent; you can access them from different computers at different times or even simultaneously.