OmniBioAI
AI-Powered Bioinformatics Platform with registry-driven plugins and reproducible workflows
Plugins
Choose a category to focus the launcher.
Dashboard
8 app(s)
Alerting & Notifications
Threshold-based alerts, notifications, and alert history for OmniBioAI
System Health
Celery workers, queue depth, failed tasks, and disk/temp usage.
Provenance
Audit trail & lineage for OmniObjects (reproducible workflows)
Resource & Cost Monitoring
Track compute usage and cloud costs across projects and teams
Dataset Catalog
Central catalog of datasets: versions, size, freshness, schema, and lineage links
Audit & Activity Log
Platform-wide audit trail and activity timeline across OmniBioAI services
Data Manager
Upload, organize, and manage datasets & OmniObjects
Plugin Manager
Admin UI to enable/disable plugins and regenerate compiled outputs
Workflows
5 app(s)
Workflow Dashboard
Monitor real-time progress of workflows and long-running tasks.
Workflow Runner
Generic registry-backed workflow execution UI with shared templates and services
Workflow Builder
Canvas-based drag-and-drop workflow builder for authoring reproducible pipelines
Visual Workflow Explorer
Interactive DAG-based explorer for WDL/Nextflow/Snakemake/CWL workflows
Workflow Registry Admin
Admin UI for registering workflow bundles
AI
4 app(s)
OnboardAI
Project documentation browser (plugins + docs) with Markdown rendering
Agent Workflow Studio
Visual studio for designing, previewing, and running agent workflows
OmniBioAgent OS
Autonomous AI system for bioinformatics workflows (intent → DAG → execution).
Literature RAG
Search PubMed, retrieve evidence, and generate grounded summaries with citations.
Analysis
4 app(s)
RNA-seq Analysis Intelligence
Differential expression and downstream intelligence from RNA-seq workflow outputs (DESeq2, QC, plots)
Exome Analysis
Exome sequencing pipelines and interpretation helpers
Metabolomics Analysis
Metabolomics pipeline scaffolds and reporting
Proteomics
Proteomics / Mass spectrometry analysis workflows
Genomics
21 app(s)
FASTQ Trimmer
Tool for trimming FASTQ files using various tools like Flexbar or Trimmomatic
FASTQ Quality Control (FastQC + MultiQC)
Standalone FASTQ quality control using FastQC and MultiQC; reusable across RNA-seq, exome, and genome workflows
Variant QC & Filtering
Stage-1 variant quality control and filtering for VCF files
BEDTools Intersect
Genomic interval intersection using bedtools intersect for overlap and annotation workflows
Polygenic Risk Score (PRS) Builder
Build and evaluate Polygenic Risk Scores (PRS) from GWAS summary stats + cohort genotypes; produces PRS scores, weights, and evaluation plots.
eQTL Linker
Variant-to-gene eQTL linking and GWAS locus overlap visualization (LocusZoom-style).
SpliceAI Variant Annotation
Deep learning-based splice site effect prediction on VCF files using SpliceAI (Illumina)
Phasing & Haplotype Analysis
Cohort-, reference-, and trio-aware genotype phasing and haplotype analysis with QC and reproducible artifacts
DeepVariant Variant Caller
DeepVariant (CPU/GPU) runner scaffold via TES/container runtime
Phenotype Association
Association analysis between genotypes and phenotypes (GWAS, PheWAS, covariate-aware models)
Rare Variant Burden Testing
Gene-based rare variant burden testing (SKAT, burden tests) with covariate-aware models and pathway enrichment
Read Simulator
Synthetic read simulator for WGS, WES, and RNA-seq. Supports single-end and paired-end layouts. Produces FASTQ and simulation manifest for benchmarking and testing pipelines.
Pathogenicity Scoring
Rank variants using SnpEff consequence/impact and optional predictors (future: CADD/REVEL/SpliceAI).
GWAS & Population Genetics
Population QC, ancestry analysis (PCA), and GWAS using containerized pipelines
Gene Annotation
Gene & functional annotation utilities
Genome Viewer
IGV-style genome visualization plugin
Network Analysis
Network and graph analysis workflows
OmniLink: Enhancer-to-Target Mapping
WIP: Variant → enhancer → gene mapping engine
Pathway Enrichment
Pathway and enrichment analysis workflows
SV/Fusion Circos (Interactive)
Interactive Circos visualization for structural variants and gene fusions with hover and filtering
Variant Annotation
VCF-based variant annotation pipelines
Machine Learning
6 app(s)
OmniML Studio
Machine learning tutorials, experiments, and model development hub
Variant Effect Intelligence
Variant annotation, pathogenicity prediction, and functional impact ranking using ML
Single-Cell Omics Intelligence
Single-cell RNA/ATAC analysis with ML-based clustering, cell-type annotation, and state inference
Single-Cell Cell Type DL
Deep learning cell-type classification for single-cell RNA-seq using PyTorch
Drug Target Intelligence
Drug–target ML inference and ranking
Histopathology Computer Vision
Whole-slide image preprocessing and CV inference
Utilities
7 app(s)
Object Registry Explorer
Browse OmniObject registry: status, sizes, paths, and metadata
OmniBioAI Catalog
Unified platform catalog of tools, workflows, plugins, and compute backends with version and capability visibility.
Ecosystem Codebase Report
Generate and view interactive codebase statistics for the full OmniBioAI ecosystem.
LIMS Integration
Integrate external LIMS (LIMS-X) with OmniBioAI for sample and project metadata
Collaboration
Multi-user collaboration, sharing, and activity
Run Inspector
Run provenance, reproducibility, and audit viewer
Circrna
3 app(s)
Clinical
2 app(s)
Epigenomics
7 app(s)
ChIP-seq QC Metrics
Extract normalized ChIP-seq QC metrics (FRiP, mapping, dup, peaks) from workflow outputs into OmniObjects.
ChIP-seq Peak Set Ops
Replicate-aware peak operations: overlap, consensus peak sets, and optional IDR integration.
ChIP-seq Peak Annotation
Annotate peaks to genes/features (promoter/intron/intergenic), generate tables and summary plots.
ChIP-seq Motif Analysis
Motif enrichment analysis from peak sequences (HOMER/MEME), returns top motifs and candidate regulators.
ChIP-seq Signal Plots
Generate deepTools plots (heatmaps, metaplots) from bigWig signal over peaks/TSS/regions.
ChIP-seq Differential Binding
Differential binding analysis between conditions (DiffBind/csaw), produces differential peaks and plots.
ChIP-seq Report Generator
Compile ChIP-seq QC + peak annotation + motifs + signal plots into a final auditable HTML/PDF report OmniObject.
Single Cell
4 app(s)
Clustering
Consumes a count matrix (upload or OmniObject), runs clustering (Scanpy), and registers clustered outputs.
Marker Identification
Deterministic identification of cluster-specific marker genes from clustered single-cell datasets
Single-Cell LOOM Viewer
Interactive visualization and annotation of single-cell datasets using LOOM format
Single Cell Analysis
scRNA-seq workflow and exploration
Spatial
6 app(s)
QC Plots (Visium)
Generate Visium QC plots from Space Ranger outputs (UMIs/genes per spot, tissue coverage, spatial overlays).
Threshold Recommendation (Visium)
Compute and validate QC thresholds (min UMIs/genes, mitochondrial %, spot filtering) and produce an approval artifact.
Spatial Analysis (Visium)
Spatial feature identification (SVGs, Moran’s I/Geary’s C, spatial autocorrelation) from Visium matrices.
Spatial Report Generation (Visium)
Generate final auditable spatial transcriptomics report (QC, thresholds, spatial features, clustering, markers) for Visium workflow runs.
Spatial Clustering (Visium)
Plugin scaffold
Spatial Marker Identification (Visium)
Plugin scaffold