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Research & Science · By davila7

70 skills found.
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1
1.Perplexity Web Search

Runs web-grounded searches through Perplexity's Sonar models over OpenRouter for current events, recent literature and cited facts beyond the model's training cutoff.

davila7/claude-code-templates33k11 repos~3.5kAutomated safety check: NotesMITtoday
2
2.Neuropixels Data Analysis

Analyzes Neuropixels recordings from SpikeGLX or Open Ephys through preprocessing, drift correction, Kilosort4 spike sorting, quality metrics and curation.

davila7/claude-code-templates33k9 repos~2.8kAutomated safety check: PassMITtoday
3
3.Scientific Venue Templates

Supplies LaTeX templates and formatting rules for journals, conferences, posters, and grant proposals, then can check a draft against them.

davila7/claude-code-templates33k9 repos~5.1kAutomated safety check: NotesMITtoday
4
4.UniProt Database Access

Queries the UniProt REST API directly to search proteins, fetch FASTA sequences, map IDs between databases and read Swiss-Prot and TrEMBL entries.

davila7/claude-code-templates33k14 repos~1.7kAutomated safety check: PassMITtoday
5
5.Scanpy Single-Cell Analysis

Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.

davila7/claude-code-templates33k15 repos~2.8kAutomated safety check: PassMITtoday
6
6.pydicom DICOM Toolkit

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

davila7/claude-code-templates33k11 repos~3.3kAutomated safety check: PassMITtoday
7
7.Arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).

davila7/claude-code-templates33k11 repos~1.7kAutomated safety check: PassMITtoday
8
8.Drugbank Database

Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data.

davila7/claude-code-templates33k10 repos~2.3kAutomated safety check: PassMITtoday
9
9.PubMed REST API Search

Searches PubMed directly through its E-utilities REST API, with guidance on Boolean and MeSH query syntax, batch retrieval and citation data.

davila7/claude-code-templates33k14 repos~3.9kAutomated safety check: PassMITtoday
10
10.RDKit Cheminformatics

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

davila7/claude-code-templates33k14 repos~5kAutomated safety check: PassMITtoday
11
11.deepTools NGS Toolkit

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-templates33k12 repos~4.5kAutomated safety check: PassMITtoday
12
12.PyMC Bayesian Modeling

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-templates33k11 repos~3.9kAutomated safety check: PassMITtoday
13
13.Clinicaltrials Database

Query ClinicalTrials.gov via API v2. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k12 repos~3.7kAutomated safety check: PassMITtoday
14
14.LaminDB Biological Data Management

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-templates33k12 repos~3.6kAutomated safety check: PassMITtoday
15
15.Biomni

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis.

davila7/claude-code-templates33k8 repos~2.4kAutomated safety check: NotesMITtoday
16
16.System Resource Detector

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-templates33k10 repos~2.4kAutomated safety check: PassMITtoday
17
17.Diffdock

Diffusion-based molecular docking. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k10 repos~3.8kAutomated safety check: PassMITtoday
18
18.PyDESeq2 Differential Expression

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-templates33k11 repos~4kAutomated safety check: PassMITtoday
19
19.Chembl Database

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

davila7/claude-code-templates33k11 repos~2.5kAutomated safety check: PassMITtoday
20
20.Cirq

Quantum computing framework for building, simulating, optimizing, and executing quantum circuits.

davila7/claude-code-templates33k11 repos~2.7kAutomated safety check: PassMITtoday
21
21.ETE Toolkit for Phylogenetic Trees

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-templates33k11 repos~4.5kAutomated safety check: NotesMITtoday
22
22.openFDA Regulatory Data Queries

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-templates33k11 repos~3.6kAutomated safety check: PassMITtoday
23
23.Gtars Genomic Interval Toolkit

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-templates33k11 repos~1.9kAutomated safety check: PassMITtoday
24
24.Histolab Whole Slide Image Tiling

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

davila7/claude-code-templates33k11 repos~5.1kAutomated safety check: PassMITtoday
25
25.Medchem Compound Filters

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-templates33k11 repos~2.5kAutomated safety check: PassMITtoday
26
26.NeuroKit2 Biosignal Processing

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

davila7/claude-code-templates33k11 repos~3kAutomated safety check: PassMITtoday
27
27.Pathml

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data.

davila7/claude-code-templates33k11 repos~1.9kAutomated safety check: PassMITtoday
28
28.PyHealth Clinical ML Toolkit

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

davila7/claude-code-templates33k11 repos~4.4kAutomated safety check: PassMITtoday
29
29.Pyopenms

Python interface to OpenMS for mass spectrometry data analysis.

davila7/claude-code-templates33k11 repos~1.4kAutomated safety check: PassMITtoday
30
30.scikit-survival Time-to-Event Modeling

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-templates33k11 repos~3.7kAutomated safety check: PassMITtoday
31
31.Anndata

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-templates33k11 repos~2.5kAutomated safety check: PassMITtoday
32
32.Geniml

This skill should be used when working with genomic interval data (BED files) for machine learning tasks.

davila7/claude-code-templates33k11 repos~2.5kAutomated safety check: PassMITtoday
33
33.Pubchem Database

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k11 repos~4.1kAutomated safety check: PassMITtoday
34
34.Scvi Tools

This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities.

davila7/claude-code-templates33k11 repos~1.8kAutomated safety check: PassMITtoday
35
35.USPTO Patent and Trademark Data

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

davila7/claude-code-templates33k11 repos~4.6kAutomated safety check: PassMITtoday
36
36.Bioservices

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

davila7/claude-code-templates33k10 repos~2.5kAutomated safety check: PassMITtoday
37
37.Cosmic Database

Access COSMIC cancer mutation database. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k10 repos~2.5kAutomated safety check: PassMITtoday
38
38.Deepchem

Molecular machine learning toolkit. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k10 repos~4.4kAutomated safety check: PassMITtoday
39
39.Ensembl Database

Query Ensembl genome database REST API for 250+ species. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k10 repos~2.1kAutomated safety check: PassMITtoday
40
40.Gene Database

Query NCBI Gene via E-utilities/Datasets API. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k10 repos~1.6kAutomated safety check: PassMITtoday
41
41.Pytdc

Therapeutics Data Commons. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k10 repos~3.2kAutomated safety check: PassMITtoday
42
42.Clinical Reports

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation…

davila7/claude-code-templates33k11 repos~9.9kAutomated safety check: NotesMITtoday
43
43.FluidSim CFD Simulations

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-templates33k9 repos~2.3kAutomated safety check: PassMITtoday
44
44.Qiskit

Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits.

davila7/claude-code-templates33k9 repos~2.2kAutomated safety check: PassMITtoday
45
45.Datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults.

davila7/claude-code-templates33k13 repos~4.7kAutomated safety check: PassMITtoday
46
46.Scikit Bio

Biological data toolkit. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates33k13 repos~3.7kAutomated safety check: PassMITtoday
47
47.Biopython

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

davila7/claude-code-templates33k12 repos~3.4kAutomated safety check: PassMITtoday
48
48.Denario

Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication.

davila7/claude-code-templates33k8 repos~1.5kAutomated safety check: NotesMITtoday

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