:: DESCRIPTION
Stubb uses a probabilistic model and a maximum likelihood approach to efficiently detect cis-regulatory modules over genomic scales.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W555-9.
Stubb: a program for discovery and analysis of cis-regulatory modules.
Sinha S, Liang Y, Siggia E.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
Cis-regPred predicts intrinsically disordered protein regions that may regulate protein function by mediating interactions in cis.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Yeon JH, Heinkel F, Sung M, Na D, Gsponer J.
Systems-wide Identification of cis-Regulatory Elements in Proteins.
Cell Syst. 2016 Feb 24;2(2):89-100. doi: 10.1016/j.cels.2016.02.004. Epub 2016 Feb 24. PMID: 27135163.
:: DESCRIPTION
cis-Browser (cis-Regulatory Browser) is genome browser for cis-regulatory information inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation
::DEVELOPER
The Istrail Laboratory of Brown University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2010;674:369-99. doi: 10.1007/978-1-60761-854-6_22.
Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks.
Istrail S, Tarpine R, Schutter K, Aguiar D.
