Softwares
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]
Pipelines
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 [中戸, 実験医学, 2021年])
Database
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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