TRIPOD

Nonparametric interrogation of transcriptional regulation in single-cell RNA and chromatin accessibility multiomic data

Author

Yuchao Jiang, Yuriko Harigaya, Nancy R. Zhang

Maintainer

Yuchao Jiang yuchaoj@email.unc.edu

Description

TRIPOD is a statistical framework for detecting three-way regulatory relationships between a cis-regulatory region, a transcription factor, and a target gene, which we call a "trio," using single-cell ATAC/RNA multiomic data. The main functionality of this package is as follows.

• Infers trio regulatory relationships using robust nonparametric models
• Builds RNA prediction models from ATAC-seq data
• Identifies influential cell types in which a trio regulatory relationship is active

Installation

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

Vignettes

The vignettes for the PBMC data provide a brief overview of the data analysis using the TRIPOD package, whereas those for the mouse embryonic brain data contain detailed descriptions of the procedure.

• Preprocessing - PBMC
• TRIPOD - PBMC
• Preprocessing - mouse embryonic brain
• TRIPOD - mouse embryonic brain

Issues & bugs

Please do not email but post here on GitHub for fastest reply/help.

Common questions

• What if my TF/motif of interest is not included in the default annotation?
• Annotated motifs in addition to the JASPAR database?
• How to handle multiple TFs with the same motif?

Manuscript code

• 10X Genomics PBMC
• 10X Genomics mouse embryonic brain
• SHARE-seq mouse skin
• SNARE-seq adult mouse brain

Reference

Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy R Zhang. Nonparametric single-cell multiomic characterization of three-way relationships between transcription factors, target genes, and chromatin accessibilities. Cell Systems, 13 (9), 737-751, 2022. (link)