OMIX

OMIX is an R bioinformatics monorepo. It combines an installable shared R package with independent analysis modules.

OMIX/
|-- core/                              Shared R package: Omix
|-- modules/                           Independent analysis modules
|   |-- OMIX-GSEA-Preranked-Legacy/
|   |-- OMIX-L2P-Single/
|   `-- OMIX-L2P-Multi/
|-- docs/                              Repository and module conventions
`-- tests/                             Repository-level contract checks

core/ is the installable Omix package. It currently provides reusable color palette utilities, including get_color_palette().

For analysis use, install it directly from GitHub:

install.packages("remotes")
remotes::install_github("NIDAP-Community/Omix", subdir = "core")
library(Omix)

See core/README.md for the full utility guide and local contributor setup.

Each directory under modules/ is independent from the other modules and from the Omix package API. It owns its own source, tests, schemas, documentation, and release history.

Each module will be synchronized with its corresponding individual repository. The synchronization tooling is under construction.

The Module link below is the canonical, platform-neutral implementation. The Code Ocean adapter link is the repository deployed as a capsule; it contains the Code Ocean-specific code/, metadata, and environment files.

Read docs/module-contract.md before adding or releasing module implementation.

Shared runtime definitions live in starter-environments/. They are built once for a scientific domain and then used by module-specific container overlays. This keeps pathway modules independent of MOSuite while allowing the same pinned OCI image to run in Code Ocean, Docker, and HPC. See docs/starter-environments.md.

Run the repository layout check from the repository root:

Rscript tests/test-monorepo-layout.R

Run the core package tests after installing its dependencies:

testthat::test_local("core")