cassiopeia Cas9-Enabled single cell lineage tracing tree reconstruction compass Metabolic modeling using single-cell transcriptomes epitome Prediction of epigenetic events using chromatin accessibility hotspot A tool for identifying informative genes (and gene modules) in a single-cell dataset. ImpulseDE Differential expression for time-course data. MPRAnalyze Statistical framework for data generated by MPRAs scone Framework for the evaluation of scRNA-seq normalization scvi-tools single-cell variational inference tools symsim Simulation of single-cell RNA-Seq data trapes + brapes TCR + BCR reconstruction algorithms for paired-end data VISION Functional interpretation for scRNA-seq data