2 Preface and Overview
3 Preface and Overview
3.1 CDI Omics Systems
CDI Omics Systems is an evolving ecosystem of structured omics workflows designed to connect:
- raw biological data
- analytical processing
- statistical reasoning
- interpretation
- reproducible reporting
The focus is not only on running tools, but on building complete analytical systems that support transparent and defensible biological insight.
4 An Evolving Omics Ecosystem
CDI Omics Systems is designed as a modular and continuously expanding ecosystem of reproducible analytical systems.
Each build represents a connected workflow architecture focused on:
- reproducibility
- workflow transparency
- interpretation-first analysis
- systems-oriented biological reasoning
Some builds are actively expanding as the ecosystem evolves.
5 Systems Over Outputs
Many workflows stop at generating outputs.
CDI Omics Systems emphasizes:
Data
→ Processing
→ Exploration
→ Statistical analysis
→ Interpretation
→ ReportingEach build is designed to function as a connected system rather than an isolated tutorial.
6 Omics System Builds
6.1 Build 01 · RNA-seq System
End-to-end transcriptomics workflows integrating:
- FastQC
- MultiQC
- Salmon / STAR
- featureCounts
- DESeq2
- exploration and visualization
- Quarto reporting
6.2 Status
Active flagship build.
6.3 Live Build
rnaseq.complexdatainsights.com
6.4 Build 02 · Microbiome System
Structured microbiome analysis systems integrating:
- denoising
- taxonomy assignment
- ecological analysis
- diversity analysis
- interpretation workflows
6.5 Status
Active build.
6.6 Live Build
microbiome.complexdatainsights.com
6.7 Build 03 · GWAS System
Genome-wide association workflows integrating:
- genotype quality control
- population structure
- association testing
- variant interpretation
6.8 Status
Active build.
6.9 Live Build
6.10 Build 04 · Single-cell RNA-seq System
Single-cell systems integrating:
- normalization
- clustering
- dimensional reduction
- annotation
- cellular interpretation
6.11 Status
Active build.
6.12 Live Build
singlecell.complexdatainsights.com
6.13 Build 05 · Multi-omics Integration System
Integrated systems connecting:
- transcriptomics
- microbiome
- clinical metadata
- statistical modeling
- interpretation layers
6.14 Status
Expanding build.
6.15 Live Build
multiomics.complexdatainsights.com
7 Workflow Philosophy
CDI Omics Systems emphasizes:
- reproducibility
- interpretation-first analysis
- workflow transparency
- modular systems architecture
- defensible analytical reasoning
The ecosystem is intentionally designed to evolve progressively as individual builds expand.
8 Technology Ecosystem
Depending on the build, workflows may integrate:
- R
- Python
- Bioconductor
- Quarto
- Plotly
- QIIME2
- Scanpy
- GitHub Pages
- reproducible environments
9 CDI
Complex Data Insights (CDI)
Systems over outputs.