Research & Science · Python

Cloud-based quantum chemistry platform with Python API. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

Reads, edits, anonymizes and converts DICOM medical imaging files with pydicom, including pixel data extraction and compressed transfer syntaxes.

davila7/claude-code-templates

Guides mechanistic interpretability work with TransformerLens: loading models, caching activations, using HookPoints, activation patching and attention-pattern analysis.

Orchestra-Research/AI-Research-SKILLs

End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.

QING1105/ezST

The opencode binding of the AutoMCM-Pro math modeling pipeline for CUMCM and MCM/ICM contests, with tool mappings, install prompts and checkpointed runs.

RealSeaberry/AutoMCM-Pro

Author, package, validate, or run mathematical evaluations as Jacobian Harbor datasets.

morluto/jacobian

Access and configure a user's local or cloud Zotero library without MCP by executing the bundled JSON CLI.

Bubble-OoO/zotero-research-assistant-skill

Produce a comprehensive, referenced deep-research report on a given topic as a downloadable markdown file.

impredicative/podgenai

RDKit molecular manipulation and visualization within Coot's Python environment.

pemsley/coot

Guides molecular work with RDKit in Python: reading SMILES and SDF, sanitization, descriptors, fingerprints, substructure and similarity search, reactions and coordinates.

davila7/claude-code-templates

Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.

davila7/claude-code-templates

Interact with Zotero reference management libraries using the pyzotero Python client.

agent-skills-hub/agent-skills-hub

Clusters the latest news-feed results by topic and writes a briefing of research idea seeds with citations, plus a structured seeds file, without crawling new sources.

OpenLAIR/dr-claw

Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows.

K-Dense-AI/scientific-agent-skills

Generates publication-quality scientific figures with matplotlib or seaborn through query expansion, a run-and-retry coding loop and a visual check of the rendered PNG.

lingzhi227/agent-research-skills

Builds, fits, checks and compares Bayesian models in PyMC, from priors and NUTS sampling to variational inference, LOO and WAIC comparison, and diagnostics.

davila7/claude-code-templates

Runs flux balance analysis and related constraint-based simulations on a COBRApy metabolic model, from standard FBA to gene knockouts and carbon source swaps.

aiming-lab/AutoResearchClaw

Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.

jinzhezenggroup/computational-chemistry-agent-skills

Snapshot the computational environment for a replication package — detects the analysis stack (R / Stata / Python) and emits the right lockfiles (renv.lock + sessionInfo.txt, requirements.txt /…

pedrohcgs/claude-code-my-workflow

Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.

davila7/claude-code-templates

A skill your agent uses when the user wants an end-to-end AI4S research pipeline — broad direction or specific topic in, full research package out (exploration + literature survey + experiment +…

ai4s-research/ai4s-skills

Guides causal experiments on PyTorch models with pyvene, such as causal tracing, activation patching and interchange intervention training, to test how a model works.

Orchestra-Research/AI-Research-SKILLs

Detects CPU, GPU, memory and disk resources before heavy scientific tasks and writes a JSON file with advice on parallelism, out-of-core work and GPU use.

davila7/claude-code-templates

Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.

davila7/claude-code-templates

Query ChEMBL's bioactive molecules and drug discovery data. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Guides your agent through building, editing, comparing and drawing phylogenetic trees with the ETE Python toolkit, including orthology calls and NCBI taxonomy lookups.

davila7/claude-code-templates

Queries the openFDA API from Python for drug, device, food and veterinary data: adverse events, recalls, labels, approvals, NDC and UNII lookups.

davila7/claude-code-templates

Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.

davila7/claude-code-templates

Processes digital pathology whole slide images with histolab: tissue detection, mask creation, tile extraction and dataset preparation for deep learning.

davila7/claude-code-templates

Screens compound libraries in Python with the medchem library: drug-likeness rules, PAINS filters, structural alerts and complexity metrics for prioritizing molecules.

davila7/claude-code-templates

Processes physiological signals with NeuroKit2 in Python: ECG, PPG, EEG, EDA, respiration, EMG and EOG, including HRV, events and complexity measures.

davila7/claude-code-templates

Builds machine learning pipelines on clinical data with PyHealth: EHR datasets, prediction tasks, medical code mapping, healthcare models and evaluation.

davila7/claude-code-templates

Python interface to OpenMS for mass spectrometry data analysis.

davila7/claude-code-templates

Fits and evaluates survival models with scikit-survival: Cox models, Random Survival Forests, boosting, survival SVMs, concordance index, Brier score and competing risks.

davila7/claude-code-templates

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…

davila7/claude-code-templates

Searches USPTO patent and trademark data through its APIs: patent search, PEDS examination history, assignments, citations, office actions and TSDR status.

davila7/claude-code-templates

Drives an end-to-end workflow for the CUMCM math modeling contest: reads the problem and data, researches, codes and verifies models, then writes a LaTeX paper and PDF.

RealSeaberry/AutoMCM-Pro

Build high-quality literature reviews from a research topic using a 10-phase workflow.

Drchronx/ai-agent-research-starter-kit

Consolidates BERTopic, LDA or NMF topic output into a theory-driven classification framework and writes the final labels back to an Excel file.

TyrealQ/q-skills

Extracts research papers from .bib and .html venue files, filters them by relevance, labels them with a two-level taxonomy through Claude and rebuilds a website.

PurCL/ASE

Primary Python tool for 40+ bioinformatics services. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Use ChemGraph Python and CLI workflows, agent-written batch scripts, and attached chemistry MCP tools.

argonne-lcf/ChemGraph

生成研究/项目架构图、流程图、层次图（swimlane / processflow / hierarchytree）。适合 PPT 汇报、技术文档、综述插图。输出风格接近 draw.io，可选 graphviz（高质量）/ matplotlib（零依赖）双后端。

csmar432/finai-research

Turns raw flux balance analysis output and a COBRApy model into gene essentiality maps, phenotypic phase planes, flux sampling results, pathway summaries and secretion predictions.

aiming-lab/AutoResearchClaw

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