Research & Science · Python

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

davila7/claude-code-templates

Parses a math modeling contest problem from PDF, Word or pasted text and produces a task breakdown, paper outline, scoring map and model route for each question.

yushui2022/MathModel-Skill

Diagnose a brand, website, or page for evidence-backed GEO gaps and opportunities from user-supplied URLs, HTML, or evidence.

yaojingang/GEOHub

Stage protocol for a math-modeling pipeline that turns a problem analysis into a unified mathematical mechanism, formulas, a solution route and a validation plan.

WuXinbo-bo/Math-model-skills

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

3Dmol.js WebGL molecular visualization emitted as self-contained HTML.

jaechang-hits/SciAgent-Skills

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

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

Extract reusable Jacobian capabilities from a mathematical solution corpus, rather than one agent trajectory.

morluto/jacobian

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

Packages standalone FHIR R4 resources from OpenMed output into one transaction Bundle with stable fullUrls and rewritten references, ready to post to a FHIR server.

maziyarpanahi/openmed

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

MingfengHong/paperseek

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

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

K-Dense-AI/scientific-agent-skills

Runs a math modeling competition entry end to end, in AI-led or human-led mode, with Git checkpoints and self-verified solver code before it enters the LaTeX paper.

RealSeaberry/AutoMCM-Pro

Searches Reddit posts by meaning through the reddapi.dev index, with topic momentum and subreddit lookup, to research how people describe problems and compare tools.

lignertys/reddit-research-skills

Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO.

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

Measure GEO visibility from an approved, file-backed engine observation bundle.

yaojingang/GEOHub

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

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

Tracks physical units and propagates measurement uncertainty in scientific calculations using pint and uncertainties.

K-Dense-AI/scientific-agent-skills