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A python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering >80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles.

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Methyl-Analyzer classification

Methyl-Analyzer specifications

Software type:
Restrictions to use:
Input format:
Mates format (SOLiD platform), SAM
Output format:
BED, Wiggle, Microarray formats
Programming languages:
Computer skills:
Numpy, Pyfasta, Pysam
Command line interface
Input data:
Aligned and paired-end reads to a reference genome
Output data:
Recognition sites, estimate methylation scores, DNA methylation profiles
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0

Methyl-Analyzer distribution


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Methyl-Analyzer support



  • Fatemeh G. Haghighi <>


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Department of Psychiatry, Columbia University, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA; Department of Neurology, Mount Sinai School of Medicine, New York, NY, USA

Funding source(s)

National Institute of Health (NIH) (HG002915); National Institute of Mental Health (NIMH) (MH074118)

Link to literature

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