{"repo":"saeyslab/nichenetpy","free":true,"listed":false,"github":"https://github.com/saeyslab/nichenetpy","clone":"git clone https://github.com/saeyslab/nichenetpy.git","description":null,"language":"Jupyter Notebook","stars":15,"topics":["cell-cell-communication","data-integration","gene-expression","intercellular-communication","ligand-receptor","ligand-target","network-inference","rna-seq","single-cell-omics","single-cell-rna-seq"],"license":"BSD-3-Clause","category":"data-pipelines","readme_excerpt":"NicheNetPy: the python implementation of the NicheNet method. (ported from NicheNetR) 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. Installation of nichenetpy Overview of NicheNet Background NicheNet strongly differs from most computational approaches to study cell-cell communication (CCC), as summarized conceptually by the figure below ( top panel: current ligand-receptor inference approaches; bottom panel: NicheNet). Many approaches to study CCC from expression data involve linking ligands expressed by sender cells to their corresponding receptors expressed by receiver cells. However, functional understanding of a CCC process also requires knowing how these inferred ligand-receptor interactions result in changes in the expression of downstream target genes within the receiver cells. Therefore, we developed NicheNet to consider the gene regulatory effects of ligands. At the core of NicheNet is a prior knowledge model, created by integrating three types of databases—ligand-receptor interact","default_branch":null,"files":null,"tree":[],"storefront":"/r/saeyslab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/saeyslab/nichenetpy/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."}