James Shiniti Nagai

James Shiniti Nagai

Machine Learning, Complex Network, Computational Biology and Bioinformatics

Tools and Resources

scMEGA

Published:

scMEGA Fantastic work from Zhijian Li(https://lzj1769.github.io/). scMEGA(Single-cell Multiomic Enhancer-based Gene regulAtory network inference) is a R package designed to infer gene regulatory network by using single cell multi-omics data. It is based on several popular packages for single cell RNA/ATAC-seq data analysis, particularly, Seurat, Signac, and ArchR. Picture below showed the principal of scMEGA for linking genes to TFs and building a gene regualtory network.

CrossTalkeR

Published:

CrossTalkeR is a framework for network analysis and visualisation of LR networks. CrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of CrossTalkeR for characterisation of changes in cellular crosstalk in disease state.