OMIX

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

OMIX/
|-- core/                              Shared R package: Omix
|-- bridges/                           Optional ecosystem-specific R packages
|   |-- mosuite/                       OmixMOSuite MOO-to-table bridge
|   `-- seurat/                        OmixSeurat pseudobulk bridge
|-- modules/                           Independent analysis modules
|   |-- OMIX-GSEA-Preranked-Legacy/
|   |-- OMIX-DEG-Analysis/
|   |-- OMIX-L2P-Single/
|   `-- OMIX-L2P-Multi/
|-- docs/                              Repository and module conventions
`-- tests/                             Repository-level contract checks

Core package

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.

Optional bridge packages

bridges/ contains separately installable packages that convert a supported external data object into a portable Core contract. They are not dependencies of Omix or ordinary table-based modules.

Package	Ecosystem	Purpose
OmixMOSuite	MOSuite	Convert an MOO into omix_standard_input counts and metadata tables.
OmixSeurat	SeuratObject	Aggregate one selected cell type into donor-by-condition raw-count pseudobulk tables.

See bridges/README.md for the extension contract and installation guidance.

Module catalog

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.

The Module link below is the canonical, platform-neutral implementation. The optional Deployment repository link is a separately maintained interface and runtime layer; it is not required to run the module locally.

Module	Deployment repository	Purpose	Status
OMIX-DEG-Analysis	OMIX-DEG-Analysis	Raw-count differential expression	Review
OMIX-GSEA-Preranked-Legacy	OMIX-GSEA-Preranked-Legacy	Legacy preranked GSEA	Active
OMIX-Volcano-Plot	OMIX-Volcano-Plot	Differential-expression volcano plot	Active
OMIX-L2P-Single	OMIX-L2P-Single	Single-comparison L2P	Active
OMIX-L2P-Multi	OMIX-L2P-Multi	Multi-comparison L2P	Active

Read the developer guide and module contract before adding or releasing module implementation. The compact instructions for GitHub Copilot are in .github/copilot-instructions.md.

Starter environments

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 locally, in Docker, and on HPC. See docs/starter-environments.md.

Checks

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")