NicheNet: predict active ligand-target links between interacting cells
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Updated
Sep 5, 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
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.
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.
LIANA x Tensor-cell2cell Protocols
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
Domain Adaptive and Fine-grained Anomaly Detection for Single-cell Sequencing Data and Beyond
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