HiC1Dmetrics: Framework to extract various 1D features from Hi-C data [Wang and Nakato, Briefing in Bioinformatics, 2021]

EEISP - Identifying codependent and mutually exclusive gene sets from sparse scRNA-seq data [Nakajima et al., Nucleic Acids Research, 2021]

DROMPAplus - An new version of DROMPA that has many valuable features [Nakato and Sakata, Methods, 2020]

SSP - Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile [Nakato and Shirahige, Bioinformatics, 2018]

DROMPA - Peak-calling and Visualization Tool for Multiple ChIP-seq Data [Nakato and Shirahige, Methods in Molecular Biology, 2018]

Cgaln - Fast and space-efficient whole-genome alignment [Nakato and Gotoh, BMC Bioinformatics, 2010]


Churros: ChIP-seq analysis pipeline

RumBall: RNA-seq analysis pipeline

CustardPy: Hi-C analysis pipeline [Nakato et al., bioRxiv, 2022]

ShortCake: a Docker image for single-cell analyses (a new version of singlecell_jupyter [’†ŒË, ŽÀŒ±ˆãŠw, 2021”N])


CohesinDB: a comprehensive database for cohesin analysis [Wang and Nakato, Nucleic Acids Research, 2022]

Epigenome and transcriptome database for human vascular endothelial cells [Nakato et al., Epigenetics & Chromatin, 2019]

Documents (in Japanese)

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