README.md

In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

InterCellDB

InterCellDB is a tool for analyzing intercellular communication on single-cell RNA sequencing (scRNA-seq) data. It is designed for highly user-defined analysis in specific biological context. To accomplish this, InterCellDB integrates not only protein-protein interaction database, but also several databases on interaction properties (type, direction, effect) as well as gene product properties (subcellular locations, molecular functions, involving biological process).

Key features:

• Covering human and mouse
• Gene subset selection by subcellular location, molecular function and involving biological process
• Gene pair (inferred from protein-protein interactions) subset selection by type, direction and effect

Main Functions:

• Full network analysis, which summarises the interactions between every 2 cell clusters
• Intercellular analysis on action relations, which shows the composition of action mode and effect between given 2 cell clusters
• Intercellular analysis on filtering gene pairs, which extracts top ranked significant gene pairs for downstream analysis
• Intercellular analysis on specificity, which evaluates co-occurences of gene pair across interactions
• Intercellular analysis on spatial pattern, which shows the summary of target gene pairs with their attributes

Installation

1. remove the 'GO.db' package

remove.packages("GO.db")

1. install the required packages and re-intall 'GO.db' package from Bioconductor

install.packages("devtools")
install.packages("BiocManager")
BiocManager::install(pkgs = "GO.db")

1. install the InterCellDB package from GitHub

devtools::install_github("ZJUDBlab/InterCellDB")

Tutorials

Please use package-release version 0.9.2 to run all the codes. - Running InterCellDB step-by-step

Resources

All the code and data used for processing of data sources and following analysis are available in figshare, whose links are given as follows (suitable for release v0.9.2): 1. Database generation a) Mouse: https://doi.org/10.6084/m9.figshare.17057342 b) Human: https://doi.org/10.6084/m9.figshare.17057339 2. Comparison of InterCellDB and previous methods (Figure 4 related codes): a) Database comparison: https://doi.org/10.6084/m9.figshare.17057357 b) Performance comparison: https://doi.org/10.6084/m9.figshare.17057525 3. Case studies on human and mouse data a) Human example data processing (Figure 3 and S1 related codes): https://doi.org/10.6084/m9.figshare.17029997 b) Mouse example data processing (Figure 2 and S1 related codes): https://doi.org/10.6084/m9.figshare.17029985

How to cite

Jin Z,Zhang X,Dai X,Huang J,Hu X,Zhang J, Shi L. InterCellDB:a user-defined database for inferring intercellular networks. Adv Sci (Weinh). 2022 Aug;9(22):e2200045.

ZJUDBlab/InterCellDB documentation built on March 19, 2023, 4:56 p.m.