LIGER (Linked Inference of Genomic Experimental Relationships)
https://github.com/welch-lab/liger
PyLiger: Scalable single-cell multi-omic data integration in Python
https://github.com/welch-lab/pyliger
MultiVelo: Single-cell multi-omic velocity inference
https://github.com/welch-lab/MultiVelo
VeloVAE: Bayesian Inference of RNA Velocity from Multi-Lineage Single-Cell Data
https://github.com/welch-lab/VeloVAE
PerturbNet: predicting single-cell responses to perturbations
https://github.com/welch-lab/PerturbNet
MorphNet: predicting cell morphology from single-cell gene expression
https://github.com/welch-lab/MorphNet
MichiGAN (Sampling from Disentangled Representations of Cell Identity using Generative Adversarial Networks)
https://github.com/welch-lab/MichiGAN
SquiggleNet (Real-Time, Direct Classification of Nanopore Signals)
https://github.com/welch-lab/SquiggleNet
MATCHER (Manifold Alignment to Characterize Experimental Relationships)
https://github.com/jw156605/MATCHER
SLICER (Selective Locally Linear Inference of Cellular Expression Relationships)
https://github.com/jw156605/SLICER
SingleSplice algorithm for detecting alternative splicing in a population of single cells
https://github.com/jw156605/SingleSplice
AppEnD tool for mapping 3’ additions from RNA-seq data