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

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

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

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

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

A Julia package for single cell and spatial data analysis

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 Library for Denoising Single-Cell Data with Random Matrix Theory

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

DECIPHER for learning high-fidelity disentangled embeddings from spatial omics 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) and Proximity Network (PNA) assays.

Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)