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

Simulating single-cell data using gene regulatory networks 📠

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

Find causal cell-types underlying complex trait genetics

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.

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

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)