Research & Science · Python · By davila7

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

davila7/claude-code-templates

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-templates

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

davila7/claude-code-templates

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

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

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

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

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

davila7/claude-code-templates

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

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

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

davila7/claude-code-templates