NicheNet: predict active ligand-target links between interacting cells
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Updated
May 3, 2024 - R
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 🦕
Find causal cell-types underlying complex trait genetics
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
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
BANKSY: spatial clustering
R Package for Single-Cell Dataset Processing and Visualization
An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data
Simulating single-cell data using gene regulatory networks 📠
Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
Website for the fibroblast clonality project conducted at EMBL-EBI and the Wellcome Sanger Institute ca 2017-2019.
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
The software of Pamona, a partial manifold alignment algorithm.
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.
LIANA x Tensor-cell2cell Protocols
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
A Julia package for single cell and spatial data analysis
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