Software

RLR_transform

R · Research code

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

Published as scripts rather than an R package.

GitHub

CRiSM

Python · Prototype

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

The README identifies this as a prototype. See the repository for setup instructions.

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.

Some instructions need updating; the complete workflow has not been revalidated in a current environment.

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