Single cell RNA-Seq

• northstar: clustering cells on the shoulders of giants
• singlet: scRNA-Seq data exploration, by humans for humans

Genomics and transcriptomics

• HTSeq: high-throughput sequencing data analysis with long genomes and gene expression counting

Viral evolution

• FFPopSim: forward simulations of viral genome evolution via Fast Fourier Transforms
• hivwholeweb: web application for intrapatient evolution of the human immunodeficiency virus (HIV)

Graph theory

• igraph: Efficient library for the analysis of graphs/networks