NicheNet: predict active ligand-target links between interacting cells

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Papers with code for single cell related papers

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕

BANKSY: spatial clustering

Find causal cell-types underlying complex trait genetics

Simulating single-cell data using gene regulatory networks 📠

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

R Package for Single-Cell Dataset Processing and Visualization

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

A Library for Denoising Single-Cell Data with Random Matrix Theory

Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

A Julia package for single cell and spatial data analysis

Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

The software of Pamona, a partial manifold alignment algorithm.

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.

resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data

Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments