Software

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

https://github.com/jw156605/append