operon
Bioinformatics analysis protocols and research workspace for scientists
All Skills in This Repository (150)
Pure Emerald Level Indicators
swaruplabmetabolomics-workbench-database
Retrieve Metabolomics Workbench studies, compounds, and RefMet data via REST API.
swaruplabpolars-bio
Perform genomic interval operations and stream BED/VCF/BAM/GFF files with Polars and DataFusion.
swaruplabbenchling-integration
Automate Benchling registry, inventory, ELN, and workflow operations via APIs.
swaruplabnetworkx
Create, manipulate, and analyze graphs with NetworkX in Python.
swaruplabanndata
Manage AnnData structures for single-cell analysis with h5ad and zarr I/O.
swaruplabscikit-survival
Perform censoring-aware survival analysis with Cox, ensemble, and SVM models in Python.
swaruplabqiskit
Build, simulate, and execute quantum circuits on IBM Quantum hardware.
swaruplabuspto-database
Aggregate patent and trademark data from USPTO APIs for IP analysis.
swaruplabscientific-brainstorming
Facilitate structured scientific brainstorming with phase-based ideation and adaptive techniques.
swaruplabkegg-database
Query KEGG REST endpoints for pathway, gene, compound, and drug data.
swaruplabpymc
Build and infer Bayesian models with PyMC using MCMC and variational inference.
swaruplabpaper-2-web
Convert LaTeX or PDF academic papers into websites, videos, and posters.
Frequently Asked Questions
FAQPage SchemaHow to install Operon?โผ
Run `npx skills add swaruplab/operon --all -g -y` in your terminal to install all protocols globally.
What bioinformatics analyses does Operon support?โผ
It covers RNA-seq, single-cell analysis, ATAC-seq, spatial transcriptomics, metabolomics, and survival analysis through ready-made protocols.
Can Operon run analyses on HPC clusters?โผ
Yes. It connects to remote clusters via SSH and tmux, running jobs directly on compute nodes while your data stays on the server.
Which biological databases can I query with Operon?โผ
It includes integrations for KEGG, COSMIC, GEO, AlphaFold, ZINC, HMDB, JASPAR, InterPro, PubMed, and dozens more.
Do I need programming experience to use Operon?โผ
No. You describe your analysis in plain English and the agent selects and runs the right protocol for you.
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