Software

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