software

Deep learning-based spot detection for fluorescence microscopy with subpixel accuracy. For more information visit the Spotiflow GitHub

Unified Mass Imaging Analyzer for spatial lipidomics. For more information visit the uMAIA GitHub

Statistical inference with a manifold-constrained RNA velocity model. For more information visit the VeloCycle GitHub

A package for the analysis of expression dynamics in single cell RNA seq data. For more information go to the velocyto homepage

A tool for building analysis pipeline for big single cell RNA sequencing projects

Core implementation the standard format to store and work with single cell expression data. For more information go to the loompy homepage

Negative binomial generalized linear model for single cell expression data

An alternative, lightweight, python interface to the Bayesian Modeling language Stan.

Reference implementation of the clustering algorithm described in Zeisel et al. 2015

An older file format designed to store smaller single-cell RNA seq datasets