General resources

• Single-cell best practices, an evolving online textbook on best practices of single-cell sequencing analysis
• scanpy documentation
• Seurat documentation

Differential expression and abundance

• A guide to creating design matrices for gene expression experimentes

Miscellaneous topics

• In-depth discussion of knee plots and problems underlying their pathologies
• A blog post on choosing the right clustering resolution (Jean Fan)
• Another blogpost on choosing the right clustering resolution (Valentine Svensson)