- Massively parallel sequencing
- Single-cell RNA-sequencing
- CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing
- SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
- CCIPCA for R: An R implementation of Candit Covariance-free Incremental Principal Component Analysis
- Epigenome
- chipgps: a parser for files of GPS (Genome Positioning System) in Ruby, RubyGems
- QuGAcomp: R package for quantitative comparison of differential ChIP-seq data
- metaSeq: Meta-analysis of RNA-Seq count data in multiple studies (working with Mr. Koki Tsuyuzaki)
- MeSHR: Tools for conducting enrichment analysis of MeSH in your gene sets. (Tsuyuzaki K, Morota G., Nakazato T., and Nikaido I.)
- Single-cell RNA-sequencing
- Biological Database and API
- GeneSearchR, Full-text search in NCBI RefSeq and/or UniProt-KB on R
- BrainStars, an integrated transcriptome database of 50 brain regions (working with Dr. Takeya Kasukawa)
- FANTOM2 database, Database for Functional Annotation of Mouse (working with Dr. Takeya Kasukawa)
- Contribution to open-source activity
- BioRuby
- Bio::siRNA (BioRuby)
- R/Bioconductor
- bioconductor.jp (a mirror of the Bioconductor package repository in Japan)
- BioRuby
Laboratory for Bioinformatics Research
RIKEN Center for Biosystems Dynamics Research
