yuchaojiang / TRIPOD

Nonparametric Interrogation of Transcriptional Regulation in Single-Cell RNA and Chromatin Accessibility Multiomic Data
GNU General Public License v3.0
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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.

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.

Issues & bugs

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

Common questions

Manuscript code

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)