Perturbation Analysis in the scverse ecosystem.

CellRank: dynamics from multi-view single-cell data

A parallel ODE solver for PyTorch

R package CIDER: Meta-Clustering for Single-Cell Data Integration and Evaluation

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of dr…

A collection of best practice cookiecutter templates for all domains and languages with extensive Github support ⛺

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)

spatial transcriptome, single cell

Homepage: https://miaozhun.github.io/DEsingle. Bioconductor page: https://bioconductor.org/packages/DEsingle.

Independent Component Analysis decipher functional modules for better cell clustering and annotation

Dynamical systems methods for RNA velocity analysis

Must-read papers on deep learning based methodology paper for single cell data analysis