Installation typically takes a few minutes, depending on the number of dependencies that has already been installed on your pc. You can install nichenetr (and required dependencies) from github with: nichenetr was tested on both Windows and Linux (most recently tested R version: R 4.0.0) ...
paper, see https://github.com/saeyslab/NicheNet_LiverCellAtlas. 15-10-2019: Bonnardel, T’Jonck et al. used NicheNet to predict upstream niche signals driving Kupffer cell differentiation Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing ...
Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet ( https://github.com/saeyslab/nichenetr ), a method that predicts ligand–target links between interacting cells by combini
NicheNet(https://github.com/saeyslab/nichenetr[https://github.com/saeyslab/nichenetr])是一个计算不同细胞间相互作用的R包,通过细胞的表达数据与已知的信号和基因调控网络的相结合,预测相互作用细胞之间的配体-受体作用。通过将NicheNet应用于肿瘤和免疫细胞微环境
NicheNet(https://github.com/saeyslab/nichenetr)是一个计算不同细胞间相互作用的R包,通过细胞的表达数据与已知的信号和基因调控网络的相结合,预测相互作用细胞之间的配体-受体作用。通过将NicheNet应用于肿瘤和免疫细胞微环境数,可以推断出活性配体及其对相互作用细胞的基因调控作用。
3.https://github.com/saeyslab/nichenetr/blob/master/vignettes/faq.md END 排版人:小久 原创声明:本文由欧易生物(OEBIOTECH)学术团队报道,本文著作权归文章作者所有。欢迎个人转发及分享,未经作者的允许禁止转载。
官网:https://github.com/saeyslab/nichenetr Nature Methods原文 1. NicheNet介绍 1.1 NicheNet工作流程: 一般的预测细胞交互的软件往往只考虑sender细胞的配体和receiver细胞的受体表达,但细胞交互过程除了配体-受体相互作用以外,还包含了receiver细胞接受信号后相关通路的激活。
https://github.com/saeyslab/nichenetr 首先是文件准备,nichenet先验模型数据下载,之前它提供的链接我这里进不去了,后来网上找到了另外的链接,可直接下载到本地后读入: #ligand_target_matrix下载地址:https://zenodo./record/5518463/files/ligand_target_matrix.rds?download=1ligand_target_matrix <- readRDS("...
本文的分析数据和代码来自NicheNet官方分析单细胞数据的教程,https://github.com/saeyslab/nichenetr/blob/master/vignettes/seurat_wrapper.md 演示数据集源自Medaglia et al. 2017 “Spatial Reconstruction of Immune Niches by Combining Photoactivatable Reporters and scRNA-Seq.” Science, December, eaao4277. htt...
//github.com/hadley/httr/releases/tag/v0.3 .httr-oauth # knitr and R markdown default cache directories *_cache/ /cache/ # Temporary files created by R markdown *.utf8.md *.knit.md # R Environment Variables .Renviron # pkgdown site docs/ # translation temp files po/*~ # RStudio ...