Nonparametric interrogation of transcriptional regulation in single-cell RNA and chromatin accessibility multiomic data
Yuchao Jiang, Yuriko Harigaya, Nancy R. Zhang
Yuchao Jiang yuchaoj@email.unc.edu
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
install.packages("devtools")
devtools::install_github("yuchaojiang/TRIPOD/package")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
Please do not email but post here on GitHub for fastest reply/help.
- 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?
- 10X Genomics PBMC
- 10X Genomics mouse embryonic brain
- SHARE-seq mouse skin
- SNARE-seq adult mouse brain
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)