# Skills for Science and research Skills for Science and research: what each one does, an install command and example prompts. 676 cards · page 4 of 17 - HTML: https://affpapa.org/en/nevibecode/skills/topic/science?page=4 - Instructions for agents: https://affpapa.org/en/nevibecode/agents.md - [paperzilla](https://affpapa.org/en/nevibecode/skills/paperzilla.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill that lets your agent access Paperzilla projects, recommendations, and papers through the CLI. - [zarr-python](https://affpapa.org/en/nevibecode/skills/zarr-python.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Stores and queries chunked N-D scientific arrays with Zarr-Python 3. - [esm](https://affpapa.org/en/nevibecode/skills/esm.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill for Biohub's esm Python SDK: ESM3 protein generation, ESMC embeddings and ESMFold2 all-atom folding, run locally or through a hosted client. - [pyhealth](https://affpapa.org/en/nevibecode/skills/pyhealth.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Builds and validates PyHealth pipelines for clinical data: EHR, signals, imaging, medical codes. - [torchdrug](https://affpapa.org/en/nevibecode/skills/torchdrug.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Helps build and debug TorchDrug 0.2.1 pipelines for molecular graphs and proteins. - [pymatgen](https://affpapa.org/en/nevibecode/skills/pymatgen.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Analyzes, validates, converts, and transforms materials structures and computed data with pymatgen. - [imaging-data-commons](https://affpapa.org/en/nevibecode/skills/imaging-data-commons.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Skill for searching and downloading public medical imaging data from the NCI Imaging Data Commons repository. - [fluidsim](https://affpapa.org/en/nevibecode/skills/fluidsim.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Sets up, validates, and analyzes bounded FluidSim CFD simulations with strict resource limits and HPC safety checks. - [molecular-dynamics](https://affpapa.org/en/nevibecode/skills/molecular-dynamics.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Runs molecular dynamics in OpenMM and analyses the trajectories with MDAnalysis: RMSD, RMSF, contact maps, free energy surfaces. - [pydeseq2](https://affpapa.org/en/nevibecode/skills/pydeseq2.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Skill for differential expression analysis of RNA-seq count data. - [adaptyv](https://affpapa.org/en/nevibecode/skills/adaptyv.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Helps design protein characterization assays in Adaptyv Bio Foundry, check catalog targets, estimate run budgets, and collect test results. - [arboreto](https://affpapa.org/en/nevibecode/skills/arboreto.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Ranks candidate regulator-target pairs from expression data: GRNBoost2 with gradient boosting, GENIE3 with random forests. - [vaex](https://affpapa.org/en/nevibecode/skills/vaex.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill for columnar analysis on a single machine when data exceeds available memory. - [benchling-integration](https://affpapa.org/en/nevibecode/skills/benchling-integration.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Automates Benchling laboratory data workflows using Python SDK 1.25.0 and REST API v2. - [datamol](https://affpapa.org/en/nevibecode/skills/datamol.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Guides an agent through molecular data work with datamol and RDKit, from SMILES parsing to descriptors, clustering, and 3D conformers. - [cellxgene-census](https://affpapa.org/en/nevibecode/skills/cellxgene-census.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill for programmatic access to CZ CELLxGENE Census, a vast catalog of standardized single-cell transcriptomics data. - [deepchem](https://affpapa.org/en/nevibecode/skills/deepchem.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Builds molecular property prediction and MoleculeNet pipelines in DeepChem 2.8.0. - [deeptools](https://affpapa.org/en/nevibecode/skills/deeptools.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill that turns sequencing data into coverage tracks, QC metrics and heatmaps around TSS and peaks. - [pydicom](https://affpapa.org/en/nevibecode/skills/pydicom.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Inspects and processes local DICOM files, transfer syntaxes, and pixel data. - [astropy](https://affpapa.org/en/nevibecode/skills/astropy.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Helps an agent write and debug Astropy code for astronomy data. - [scanpy](https://affpapa.org/en/nevibecode/skills/scanpy.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill with ready-made CLI scripts for the full single-cell RNA-seq workflow: QC, normalization, clustering, marker genes, visualization. - [rdkit](https://affpapa.org/en/nevibecode/skills/rdkit.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Guides coding agents through cheminformatics tasks in Python, including SMILES parsing, descriptor calculations, and 3D coordinate generation. - [clinical-decision-support](https://affpapa.org/en/nevibecode/skills/k-dense-ai-clinical-decision-support.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Builds and checks research-only clinical decision-support artifacts: evidence profiles, cohorts, survival plans, de-identification. - [gget](https://affpapa.org/en/nevibecode/skills/gget.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Bioinformatics skill providing unified access to over 20 genomic databases via CLI and Python. - [clinical-reports](https://affpapa.org/en/nevibecode/skills/k-dense-ai-clinical-reports.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Builds draft skeletons for clinical reports and checks them with local scripts. - [anndata](https://affpapa.org/en/nevibecode/skills/anndata.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Skill to create, read, and transform annotated data matrices in h5ad and Zarr formats. - [bioservices](https://affpapa.org/en/nevibecode/skills/bioservices.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Guides Python workflows using BioServices to query biological databases. - [hypogenic](https://affpapa.org/en/nevibecode/skills/hypogenic.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Skill to plan and audit HypoGeniC, a tool that generates candidate textual hypotheses from labeled datasets using LLM. - [what-if-oracle](https://affpapa.org/en/nevibecode/skills/what-if-oracle.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Walks a research plan through what-if branches: favorable, reference, adverse and more. - [simpy](https://affpapa.org/en/nevibecode/skills/simpy.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Builds, tests, and inspects process-based discrete-event simulations using SimPy. - [geomaster](https://affpapa.org/en/nevibecode/skills/geomaster.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Guides geospatial research work with satellite imagery, vector and raster GIS data, coordinate systems, spatial statistics, and Earth observation models. - [pymoo](https://affpapa.org/en/nevibecode/skills/k-dense-ai-pymoo.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — A skill that drives pymoo from your agent: algorithm choice, problem setup, constraints and Pareto front analysis. - [scikit-bio](https://affpapa.org/en/nevibecode/skills/scikit-bio.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Analyzes biological sequences, alignments, and phylogenetic trees directly in your terminal. - [geopandas](https://affpapa.org/en/nevibecode/skills/k-dense-ai-geopandas.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Guides Python geospatial workflows using GeoPandas, audits vector geometries, and verifies CRS transformations before execution. - [research-lookup](https://affpapa.org/en/nevibecode/skills/research-lookup.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Collects verified academic articles and references for a manuscript or review when you need 60+ sources. - [biopython](https://affpapa.org/en/nevibecode/skills/biopython.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 2000 installs — Automates computational biology workflows: parses sequence files, runs alignments, and fetches records via NCBI Entrez. - [torch-geometric](https://affpapa.org/en/nevibecode/skills/torch-geometric.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 2000 installs — Guides work with PyTorch Geometric graph neural networks, from graph data setup to classification tasks. - [venue-templates](https://affpapa.org/en/nevibecode/skills/venue-templates.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 2000 installs — Prepares journal manuscripts, conference papers, research posters, and grant documents with current venue rules and bundled LaTeX scaffolds. - [open-notebook](https://affpapa.org/en/nevibecode/skills/open-notebook.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 2000 installs — Organizes research notes, citations, and document chat using self-hosted storage and AI providers. - [sr-screener](https://affpapa.org/en/nevibecode/skills/sr-screener.md) — skill · Imbad0202 · Claude Code, Codex, Cursor +3 · 469 installs — Applies protocol-driven screening to study records for reviews. Next: https://affpapa.org/en/nevibecode/skills/topic/science.md?page=5 ## Refine [research](https://affpapa.org/en/nevibecode/tag/research.md) · [python](https://affpapa.org/en/nevibecode/tag/python.md) · [bioinformatics](https://affpapa.org/en/nevibecode/tag/bioinformatics.md) · [genomics](https://affpapa.org/en/nevibecode/tag/genomics.md) · [latex](https://affpapa.org/en/nevibecode/tag/latex.md) · [citations](https://affpapa.org/en/nevibecode/tag/citations.md) · [arxiv](https://affpapa.org/en/nevibecode/tag/arxiv.md) · [pdf](https://affpapa.org/en/nevibecode/tag/pdf.md) · [api](https://affpapa.org/en/nevibecode/tag/api.md) · [machine-learning](https://affpapa.org/en/nevibecode/tag/machine-learning.md) · [markdown](https://affpapa.org/en/nevibecode/tag/markdown.md) · [pytorch](https://affpapa.org/en/nevibecode/tag/pytorch.md) ## Narrow this list Parameters: `?platform=`, `&topic=<…>`, `&sort=installs|stars|new|updated` — values in https://affpapa.org/en/nevibecode/agents.md --- NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md