Python · For researchers

Runs computational fluid dynamics simulations with the FluidSim Python framework: 2D and 3D Navier-Stokes, shallow water and stratified flow solvers plus output analysis.

davila7/claude-code-templates

Plugin shim for the mathmodel-skill competition workflow. An agent skill from handsomeZR-netizen/mathmodel-skill.

handsomeZR-netizen/mathmodel-skill

Conduct literature searches for meta-analysis using Python with uv, query PubMed and other databases, deduplicate results, and store round-based bibliographies with notes.

htlin222/meta-pipe

Use only the current SciAtlas literature-review workflow (literaturereviewpipeline) to take a novice user from zero setup to a final evidence-grounded survey outline, paper map, or literature…

zjunlp/SciAtlas

Primary Python toolkit for molecular biology. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

DNAnexus cloud genomics platform. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Latch platform for bioinformatics workflows. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.

TianGzlab/OmicsClaw

Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry.

davila7/claude-code-templates

Search Europe PMC for scientific literature and download open-access full texts and PDFs.

google-deepmind/science-skills

Chat with a companion that knows your notes folder (a journal, an Obsidian vault, any .md or .txt files) and every earlier chat, using cognee memory with local databases.

topoteretes/cognee

Sets up conference-specific LaTeX paper templates, checks a draft for formatting and submission issues, and auto-fixes common problems for venues like ICML, ICLR, NeurIPS, AAAI and ACL.

lingzhi227/agent-research-skills

Runs a deterministic, read-only health check on an Obsidian vault, reporting dead or ambiguous links, orphan pages, missing frontmatter, empty sections and stale index entries.

AgriciDaniel/claude-obsidian

Runs quality control on a COBRApy genome-scale metabolic model before flux analysis, checking mass and charge balance, biomass feasibility, dead ends, thermodynamic loops and GPR rules.

aiming-lab/AutoResearchClaw

Runs an MCM/ICM math modeling competition end to end: collects contest metadata, builds and verifies models and code, then generates an English LaTeX paper and any required memo.

RealSeaberry/AutoMCM-Pro

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam.

GPTomics/bioSkills

Analyzes one research paper in depth, writing a structured note on its methods, experiments and limitations and adding it to a paper relationship graph.

LigphiDonk/Oh-my--paper

Turns DOIs, PMIDs and arXiv IDs into clean BibTeX, searches Google Scholar and PubMed, and checks and deduplicates a reference list.

foryourhealth111-pixel/Vibe-Skills

Runs multi-source web research through Google's Gemini Deep Research Agent with a bundled Python script and saves a structured, cited report as files.

OpenLAIR/dr-claw

Zero-cost fallback for the argo search skill, wrapping 29 local engines for web, news, academic, code and reference queries when paid API quota should be saved.

taxueseek/argo

A skill your agent uses when writing academic papers, theses, or research articles - supports brainstorming, chapter writing, literature review, and LaTeX output

Norman-bury/research-writing-skill

根据REFINEDDESIGN.md中的变量定义，自动获取所需数据并生成可执行的回归分析脚本（Python/Stata）。

csmar432/finai-research

Orchestrates a research paper from literature review through code, experiments, figures, tables, writing and review, with state passed between phases and checkpoints to resume.

lingzhi227/agent-research-skills

Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.

jinzhezenggroup/computational-chemistry-agent-skills

A skill your agent uses when validating an Deep Researcher Agent change before opening or merging a PR — choosing and running the right Python, frontend, docs, or eval checks for the surfaces you…

NVIDIA-AI-Blueprints/deep-researcher-agent

Routes literature searches through the PaperSeek launcher, picks suitable scholarly sources, parses JSON output and keeps API keys out of the chat.

MingfengHong/paperseek

Build and query an evidence-lined GEO knowledge graph from approved source bundles.

yaojingang/GEOHub

Sort alignment files by coordinate or read name using samtools and pysam.

GPTomics/bioSkills

Searches arXiv by keyword, category, author or paper ID through its public API and downloads PDFs, with no API key needed.

taracodlabs/aiden

Extracts figures from a research paper, preferring the arXiv source package for original-quality images and falling back to PDF extraction.

LigphiDonk/Oh-my--paper

Sandbox approval policy blocks executecode and python3 -c; use readfile/writefile + manual transforms instead of retrying both runners.

ashutoshsinghpr7/wikiskill

Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.

jinzhezenggroup/computational-chemistry-agent-skills

Fine-tunes and evaluates OpenVLA-OFT and OFT+ robot policies with LoRA and continuous action heads on LIBERO simulation and ALOHA real-robot setups.

Orchestra-Research/AI-Research-SKILLs

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API.

K-Dense-AI/scientific-agent-skills

Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces.

K-Dense-AI/scientific-agent-skills

Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks.

K-Dense-AI/scientific-agent-skills

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP.

K-Dense-AI/scientific-agent-skills

Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs.

K-Dense-AI/scientific-agent-skills

Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots.

K-Dense-AI/scientific-agent-skills

Supports local computational pathology research with PathML: slide loading and tiling, preprocessing and QC, h5path storage, multiplex quantification, spatial graphs, and bounded model inference.

K-Dense-AI/scientific-agent-skills

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage…

K-Dense-AI/scientific-agent-skills

Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen.

K-Dense-AI/scientific-agent-skills

Builds the code for a frozen research experiment test-first, with leakage controls, seed handling and saved evidence so results can be rerun and audited.

Light0305/Light-skills

Designs custom laboratory hardware as parametric build123d models and exports fabrication artifacts as STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard…

K-Dense-AI/scientific-agent-skills

Runs the ResearchClaw 23-stage autonomous pipeline from a topic, config file and output directory, from literature review through experiments to a written and reviewed paper.

aiming-lab/AutoResearchClaw

YouTube transcript extraction and content reformatting: given a YouTube video URL, opens the video's transcript panel, extracts all timestamped segments, and transforms the raw transcript into…

browser-act/skills

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…

K-Dense-AI/scientific-agent-skills