yuchaojiang / destin2

Cross-modality dimension reduction and clustering for single-cell ATAC-seq data

Destin2: Integrative and cross-modality analysis of single-cell chromatin accessibility data

Authors

Peter Guan, Andy Lee, Lihao Wang, Yuchao Jiang

Maintainer

Peter Guan pyg at email dot unc dot edu

Description

Destin2 is a statistical framework for cross-modality dimension reduction, clustering, and trajectory reconstruction of single-cell ATAC-seq data. The main functionalities are as follows:

• Constructs cross-modality analyses of cellular-level epigenomic profiles such as peak accessibility, motif deviation, and pseudo-gene activity
• Leverages cross-modality integration for clustering, trajectory inference, and visualization

Installation

install.packages("devtools")
devtools::install_github("yuchaojiang/Destin2/package")

Vignettes

PBMC scATAC-seq by 10x Genomics

Mouse brain scATAC-seq by 10x Genomics

Issues & bugs

Please do not email but post here on GitHub for fastest reply or assistance.

Manuscript code

To ensure rigor and reproducibility, we have made our analysis scripts available. Please refer to the script folder.

Reference

Guan PY, Lee JS, Wang L, Lin KZ, Wen M, Chen L, Jiang Y. Destin2: integrative and cross-modality analysis of single-cell chromatin accessibility data. Frontiers in Genetics, 14, 1089936, 2023. (link)