Genomics Toolkits
Research skill, available on Zeplik
Genomics Toolkits is a ready-to-run research skill on Zeplik. Genomics and sequencing analysis libraries — variant calling, alignment, single-cell, population genetics, and file formats (VCF/BAM/FASTA). Ask in plain language and Zeplik applies the skill's method for you inside the conversation, on whichever AI model you prefer.
The Genomics Toolkits skill loads automatically when your request matches it, or you can invoke it directly by typing /genomics-toolkits in any chat. It works with attachments, connectors, and any model that supports the task, so you get the same expert method every time without setting anything up.
What the Genomics Toolkits skill can do
- Write runnable code for VCF, BAM, and FASTA file processing
- Perform differential gene expression analysis using pyDESeq2
- Analyze single-cell RNA-seq data with scanpy and scvi-tools
- Infer gene regulatory networks and analyze genomic interval data
Try these prompts on Zeplik
Pick a prompt to open it in the Zeplik app. If you are not signed in yet, your prompt is waiting for you the moment you do.
How the Genomics Toolkits skill works
/genomics-toolkits
Umbrella for genomics analysis libraries. The user has sequencing data and an analysis goal; establish the file format and task, pick the library, and deliver runnable code plus a rationale. For end-to-end pipeline orchestration (nf-core, scvi-tools workflows) route to bio-research-toolkit.
Dispatch table
Pick the reference file(s) that match the request, read them, then answer. Read at most 2-3 files per turn.
| Topic | Read |
|---|---|
| This skill should be used when working with annotated data matrices in Python, particul… | references/anndata.md |
| Infer gene regulatory networks (GRNs) from gene expression data using scalable algorith… | references/arboreto.md |
| NGS analysis toolkit. | references/deeptools.md |
| Parse FCS (Flow Cytometry Standard) files v2.0-3.1. | references/flowio.md |
| This skill should be used when working with genomic interval data (BED files) for machi… | references/geniml.md |
| High-performance toolkit for genomic interval analysis in Rust with Python bindings. | references/gtars.md |
| Neuropixels neural recording analysis. | references/neuropixels-analysis.md |
| Differential gene expression analysis (Python DESeq2). | references/pydeseq2.md |
| Genomic file toolkit. | references/pysam.md |
| Single-cell RNA-seq analysis. | references/scanpy.md |
| This skill should be used when working with single-cell omics data analysis using scvi-… | references/scvi-tools.md |
How to work
- Identify which leaf topic the request maps to from the dispatch table above; establish the concrete inputs (language, dataset, framework, file format) and the goal. Ask for a missing detail rather than guessing.
- Read the matching reference file(s) before answering. Read at most 2-3 per turn.
- Deliver runnable artifacts — code, configs, specs — with a short rationale, matching the user's existing conventions when they paste code.
- Confirm any decision the source flags (versions, thresholds, tradeoffs) with the user instead of guessing.
Usage
/genomics-toolkits $ARGUMENTS
How to use the Genomics Toolkits skill
Sign in to Zeplik
Create a free Zeplik account or sign in. New accounts start with free credits, so you can try the Genomics Toolkits skill right away.
Describe your research task
Ask in plain language, or type /genomics-toolkits to invoke the skill directly. Zeplik recognizes the Genomics Toolkits skill and applies its method.
Review and refine the result
Zeplik returns a clear, structured answer. Ask follow-ups in the same chat to refine it or take the next step.
Source and credit
- Author
- davila7 (D7 umbrella-consolidation)
- License
- MIT
Adapted from the open-source davila7/claude-code-templates project and tuned to run natively on Zeplik. View source on GitHub.
Frequently asked questions
- What is the Genomics Toolkits skill?
- Genomics Toolkits is a ready-to-run research skill on Zeplik. Genomics and sequencing analysis libraries — variant calling, alignment, single-cell, population genetics, and file formats (VCF/BAM/FASTA). Ask in plain language and Zeplik applies the skill's method for you inside the conversation, on whichever AI model you prefer.
- How do I use Genomics Toolkits on Zeplik?
- Sign in to Zeplik and ask in plain language, or type /genomics-toolkits in any chat to invoke it directly. The skill applies its method and returns a result you can refine in the same conversation.
- Which AI model does the Genomics Toolkits skill use?
- Any model you choose. Zeplik works across every model in one chat, so the Genomics Toolkits skill runs on your preferred model for the task.
- Where does the Genomics Toolkits skill come from?
- The Genomics Toolkits skill is adapted from the open-source davila7/claude-code-templates project (MIT) and tuned to run natively on Zeplik. The original source is linked on this page.
- How much does the Genomics Toolkits skill cost?
- Using the skill is free to start. You only spend Zeplik credits when the assistant runs, and new accounts begin with free credits.
Related research skills
- Academic PublishingAcademic publishing workflows — citation/reference management, LaTeX research posters, and venue templates with submission requirements. Use for "manage citations" or "format for a venue / make a poster"; for the writing itself see research-writing.
- Bio Research ToolkitUse when running comp-bio workflows -- single-cell RNA-seq QC, scvi-tools deep models, nf-core pipelines, instrument-to-Allotrope conversion. Not for literature research (use deep-research).
- Cheminformatics ToolkitsCheminformatics and molecular modeling — RDKit/Datamol molecular handling, DeepChem molecular ML, COBRApy metabolic modeling, Pymatgen materials, matchms/pyOpenMS mass spectrometry. Use for "work with molecules/chemistry data"; for genomics see genomics-toolkits.
- Clinical WritingClinical and medical document generation — clinical decision-support docs, clinical/case reports (CARE guidelines), and focused treatment plans in LaTeX/PDF. Use for "write a clinical report/treatment plan/CDS doc"; for research manuscripts see research-writing.
- Competitive BriefUse for competitor research or a competitive analysis -- 'compare us against X', 'build a battlecard for sales', 'competitor Y just launched Z, what does it mean for us' -- producing a positioning/messaging comparison with gaps, opportunities, threats. Not for general market reports (use deep-research).
- Deep Research ReportsUse for a long, multi-step, sourced research report -- market analysis, competitive landscaping, literature review, due diligence: 'do deep research on X', 'write a full report with citations'. Plans, searches, and synthesizes autonomously. Not for a quick look-up or short synthesis (use research).
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