{"repo":"saeyslab/nichenetr","free":true,"listed":false,"github":"https://github.com/saeyslab/nichenetr","clone":"git clone https://github.com/saeyslab/nichenetr.git","description":"NicheNet: predict active ligand-target links between interacting cells","language":"R","stars":673,"topics":["single-cell-omics","intercellular-communication","ligand-receptor","ligand-target","data-integration","single-cell-rna-seq","rna-seq","gene-expression","network-inference","cell-cell-communication"],"license":null,"category":"data-pipelines","readme_excerpt":"nichenetr nichenetr: the R implementation of the NicheNet method. (see nichenetpy for the python implementation) The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. We describe the NicheNet algorithm in the following paper: NicheNet: modeling intercellular communication by linking ligands to target genes. To help users customize NicheNet to their specific biological use-case, we have recently published a best practices workflow cultivated over four years of experience and user feedback Unraveling cell-cell communication with NicheNet by inferring active ligands from transcriptomics data. In the step-by-step protocol, we describe both a ‘sender-agnostic’ approach that considers ligands from the entire microenvironment and a ‘sender-focused’ approach that only considers ligands from cell populations of interest. We also include a new downstream procedure for prioritizing cell type-specific ligand-receptor pairs. The code to reproduce this protocol and the resulting figures can be found on . Installation of nichenetr Installation typically takes a few minutes, depending on the number of dependencies that has already been installed on your","default_branch":null,"files":null,"tree":[],"storefront":"/r/saeyslab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/saeyslab/nichenetr/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}