Research & Science · Python

gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.

affaan-m/ECC

A skill your agent uses for empirical social-science research, applied economics, public policy, education, finance, management, sociology, psychology, epidemiology, or public-health data studies.

Citrus-bit/Anaxa

Checks whether the uv Python package manager is installed and installs it if missing.

google-deepmind/science-skills

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology.

K-Dense-AI/scientific-agent-skills

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem.

K-Dense-AI/scientific-agent-skills

Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.

K-Dense-AI/scientific-agent-skills

Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and…

K-Dense-AI/scientific-agent-skills

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query…

K-Dense-AI/scientific-agent-skills

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX.

K-Dense-AI/scientific-agent-skills

Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK.

K-Dense-AI/scientific-agent-skills

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference.

K-Dense-AI/scientific-agent-skills

Processes mass spectrometry data with pyOpenMS. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation.

K-Dense-AI/scientific-agent-skills

Stores and retrieves genomic variant calls with TileDB-VCF. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and…

K-Dense-AI/scientific-agent-skills

Create and modify physics simulations using the Elodin Python SDK.

elodin-sys/elodin

Write code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity, ETKDG conformer embedding, MMFF/UFF…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab).

JimLiu/science-skills

Prepare and explain xTB semiempirical quantum-chemistry workflows for single-point energy, forces, charges, dipole, geometry optimization, and molecular dynamics.

jinzhezenggroup/computational-chemistry-agent-skills

Design and analyze studies in sociolinguistics, language variation, acoustic phonetics, discourse analysis, language contact, and computational linguistics.

joshzyj/open-scholar-skill

A skill your agent uses for AlphaFold 3 input preparation, prediction command planning, output interpretation, and Python API inspection.

VectorSpaceLab/AREX-Skill

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez).

K-Dense-AI/scientific-agent-skills

Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results.

K-Dense-AI/scientific-agent-skills

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.

K-Dense-AI/scientific-agent-skills

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis.

K-Dense-AI/scientific-agent-skills

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML.

K-Dense-AI/scientific-agent-skills

Manages Zotero reference libraries using the pyzotero Python client: retrieves, creates, updates, and deletes items, collections, tags, and attachments via the Zotero Web API v3 or local API.

K-Dense-AI/scientific-agent-skills

Typst academic paper assistant for existing .typ paper projects in English or Chinese.

brycewang-stanford/Auto-Empirical-Research-Skills

A skill your agent uses when querying biomedical databases (UniProt, ClinVar, gnomAD, PDB, Reactome, Open Targets, etc.) via the Biomni AgentCore Gateway MCP server.

aws-samples/amazon-bedrock-agents-healthcare-lifesciences

Computational molecular biology library (sequence I/O, alignment, phylogenetics).

lamm-mit/scienceclaw

Skill for academic research workflows: search Semantic Scholar (200M+ papers), inspect citations, download arXiv PDFs, and extract PDF text.

sickn33/agentic-awesome-skills

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).

ClawBio/ClawBio

Root-cause a failing or wrong empirical result with a disciplined reproduce → minimise → hypothesise → instrument → fix loop, instead of guessing-and-poking.

pedrohcgs/claude-code-my-workflow

A skill your agent uses when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels…

xuzhougeng/wisp-science

A skill your agent uses when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.

NVIDIA/skills

Multi-objective, gradient-based protein binder design with Mosaic.

adaptyvbio/protein-design-skills

A skill your agent uses when users need to search academic papers, download research documents, extract citations, or gather scholarly information.

LeoYeAI/openclaw-master-skills

Evidence-first OVITO atomistic postprocessing for LAMMPS trajectories and other particle data, including pipeline construction, modifiers, coloring, clipping, camera setup, images, animations…

Cai-aa/CAE-Agent-Hub

ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。

affaan-m/ECC

Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination…

jaechang-hits/SciAgent-Skills

Compare two implementations of the same thing — a port (R↔Python↔Stata), a reimplementation, a replication package, a refactor, or a new version against the old — so that agreement means something.

pedrohcgs/claude-code-my-workflow

Submit recoverable SSH-direct research Runs with live progress cards and model-free monitoring.

xuzhougeng/wisp-science

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results.

aipoch/medical-research-skills

Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer.

GPTomics/bioSkills

Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter.

GPTomics/bioSkills

Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables.

GPTomics/bioSkills