JRIM – Joint reconstruct cis-regulatory interaction networks of multiple cell populations

JRIM

:: DESCRIPTION

JRIM is a package for Jointly Reconstructing cis-regulatory Interaction Maps of multiple cell populations using single-cell chromatin accessibility data and identifying shared and common interaction patterns. It uses an aggregation process to deal with the sparsity of single-cell data, exploits similarity between cell types via a group lasso penalty, and generates comparable networks. JRIM could be used to characterize difference between cell types or identify dynamic changes during cell development.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

JRIM

:: MORE INFORMATION

Citation

Dong K, Zhang S.
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.
Brief Bioinform. 2021 May 20;22(3):bbaa120. doi: 10.1093/bib/bbaa120. PMID: 32578841; PMCID: PMC8138825.

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