crsky1023 / NeuronChat

NeuronChat

The goal of NeuronChat is to infer, visualize and analyze neural-specific cell-cell communication from single cell transcriptomics or spatially resolved transcriptomics data.

Installation

You can install the development version of NeuronChat like so:

devtools::install_github("Wei-BioMath/NeuronChat")

The time required for installation depends on pre-installed dependencies and the typical time is within 10 mins. Dependencies of NeuronChat package can be automatically installed when installing NeuronChat pacakge (When encountering any issues, please see the Troubleshooting section below).

Usage & Tutorial

Basic usage of NeuronChat

library(NeuronChat)
# creat NeuronChat object 
x <- createNeuronChat(normalized_count_mtx,DB='mouse',group.by = cell_group_vector) # use DB='human' for human data
# calculation of communication networks  
x <- run_NeuronChat(x,M=100)
# aggregating networks over interaction pairs
net_aggregated_x <- net_aggregation(x@net,method = 'weight')
# visualization
netVisual_circle_neuron(net_aggregated_x)

Full tutorials

A set of tutorials of NeuronChat are as follows:

• Inference, visualization and analysis of neural-specific communication network
• Analysis of spatial datasets & calculation of spatially constrained communication network
• Update the NeuronChat interaction database

These tutorials can also be found in the vignettes directory of the repo

System Requirements

Hardware requirements

NeuronChat requires a standard computer and enough memory is recommended to handle large single-cell transcriptomic datasets.

Software requirements

** Operating System Requirements

The package has been tested on the following systems:

macOS Big Sur, Version 11.5.1  
Windows 10 Pro, version 1909  

** R Dependencies (tested and recommended)

R >= 4.1.0  
dplyr >= 1.0.9
data.table >= 1.14.2  
CellChat >= 1.1.3  
Seurat >= 4.1.0  
SeuratObject >= 4.1.0  
NMF >= 0.23.0  
igraph >= 1.3.4  
ggplot2 >= 3.3.6  
ComplexHeatmap >= 2.8.0  
circlize >= 0.4.14      
ggalluvial >= 0.12.3  

Troubleshooting

Here are some instructions in case users might encounter issues during installation:

• Install CellChat using devtools::install_github("sqjin/CellChat"). See also the Installation of other dependencies in the README of CellChat for any other issues (including NMF package installation).
• Install ComplexHeatmap using devtools::install_github("jokergoo/ComplexHeatmap").
• Install circlize using devtools::install_github("jokergoo/circlize").
• Please see the instructions for installation of Seurat or SeuratObject via the link Seurat or SeuratObject.