SequenceMatrix

Generalist deep learning algorithm for cell and nucleus segmentation across diverse image types, with human-in-the-loop training (2.0) and one-click image restoration (3.0), 70K+ training objects (Nature Methods 2021/2022/2025)

Scalable genomic analysis.

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Using single-cell RNA-Seq expression to visualize CNV in cells.

Java framework for processing biological data.

Probabilistic framework for inferring cell fate decisions and trajectory dynamics from multi-view single-cell data using Markov chains and machine learning, integrating RNA velocity, pseudotime, and metabolic labeling to predict differentiation paths and terminal states (scverse/Theis Lab, 449+ stars, BSD 3-Clause)