cisASE specifications


Unique identifier OMICS_12359
Name cisASE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some DNA-seq and RNA-seq data.
Input format BAM
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Stability No
Maintained No


No version available


This tool is not available anymore.

Publication for cisASE

cisASE citation


BaalChIP: Bayesian analysis of allele specific transcription factor binding in cancer genomes

Genome Biol
PMCID: 5326502
PMID: 28235418
DOI: 10.1186/s13059-017-1165-7

[…] ich is feasible only when the coverage at any assayed heterozygous site is high (>20 × if a binomial test is to be applied to reach adequate statistical power [, ]). Recently, Liu et al. [] developed cisASE, a likelihood-based method for detecting ASE. cisASE has been shown to correct successfully for copy-number alterations that hinder the identification of ASE in RNA-seq data. Additional file : […]

cisASE institution(s)
Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA; School of Life Science and Technology, Shanghai Jiaotong University, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China
cisASE funding source(s)
Supported by the National Basic Research Program of China (2011CB910204, 2011CB510102 and 2010CB529200), the National Key Scientific Instrument and Equipment Development Project (2012YQ03026108), the National Key Technology Support Program (2013BAI101B09) and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA12000000).

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