Software

RLR_transform

R · Research code

R scripts exploring transformations of compositional time series and dynamic interaction inference using CCM (Convergent Cross Mapping), including simulations and figure-generation code.

Syntax checked for all six R scripts (September 2026). These are scripts, not an R package; the complete analyses have not been rerun.

GitHub

CRiSM

Python · Prototype

A Python CLI connecting marker-gene discovery and extraction from genomes with alignment, sequence concatenation, and phylogenetic inference.

Prototype. The published version needs fixes to invocation and error handling. The complete workflow, including external analysis tools, has not been validated.

GitHub · Usage

ShotgunMetagenomics

Docker / Shell · Tutorial (Japanese)

A Japanese-language tutorial with Shell scripts for Docker-based shotgun metagenomic analysis, covering quality control and functional profiling.

Syntax checked for all four Shell scripts (September 2026). The published setup instructions need corrections; the complete Docker workflow with real data has not been validated.

GitHub · Tutorial (Japanese)

Dockerfiles

Docker · Analysis environments

Dockerfiles for running existing bioinformatics tools in containers, including genome and metagenome analysis environments.

Provides environment definitions for existing tools.

GitHub

GitHub · DaikiKumakura