BrainPilot: Automating Brain Discovery with Agentic Research
Skill Claude CodeCodex
Domain-validated pipeline guidance for EEG/MEG data analysis using MNE-Python: data loading, preprocessing (filtering, ICA, re-referencing), epoching, ERP/ERF computation, time-frequency decomposition, source localization, decoding/MVPA, statistical testing, simulation, and visualization. Use this skill whenever the…
Skill Claude CodeCodex
Advises on functional/effective connectivity methods: PPI, DCM, Granger causality, graph theory.
Skill Claude CodeCodex
Domain-validated guidance for fMRI General Linear Model specification: HRF modeling, design matrix construction, contrast definition, confound regression, and statistical inference.
Skill Claude CodeCodex
Domain-validated guidance for fMRI preprocessing decisions: motion correction, slice timing, spatial normalization, smoothing, confound regression, and quality control.
Skill Claude CodeCodex
Guides fMRI task design: block vs. event-related vs. mixed; jittering; contrasts; power for BOLD detection.
Skill Claude CodeCodex
Preprocess task-based or resting-state fMRI data with fMRIPrep — a robust, BIDS-App preprocessing pipeline built on FSL, ANTs, FreeSurfer, AFNI, and Nilearn. Use this skill whenever the user asks to preprocess fMRI/BOLD data, run fMRIPrep on a BIDS dataset, set up Docker/Singularity/Apptainer containers for fMRIPrep…
Skill Claude CodeCodex
Domain-validated guidance for network neuroscience analysis using netneurotools: datasets, brain network metrics, connectivity consensus, modularity, spatial statistics, null models, and cortical surface visualization. Use this skill whenever the user works with brain connectivity matrices, connectomes, graph theory…
Skill Claude CodeCodex
Domain-validated methods and decision logic for neural decoding, RSA, temporal generalization, and encoding models in systems neuroscience.
Skill Claude CodeCodex
Domain-validated guidance for cortical surface visualization and brain surface rendering of fMRI data using pycortex: data types (Volume, Vertex, Dataset), 2D cortical flatmaps, 3D WebGL brain viewers, volume-to-surface mapping, FreeSurfer/fMRIPrep integration, ROI management, and surface analysis. Use this skill…
Skill Claude CodeCodex
Guides ACT-R cognitive model construction: chunk types, production rules, subsymbolic parameters, and model validation.
Skill Claude CodeCodex
Domain-validated guidance for building hierarchical Bayesian cognitive models with Stan/PyMC: prior specification, model structure, MCMC diagnostics, and posterior predictive checks.
Skill Claude CodeCodex
Guides parameter recovery studies to validate model identifiability before trusting fitted parameter values.
Skill Claude CodeCodex
Guides dimensionality reduction and latent-variable analysis of neural populations (PCA, GPFA, dPCA).
Skill Claude CodeCodex
Assists building spiking neural network simulations: neuron models, connectivity, plasticity rules.
Skill Claude CodeCodex
Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a…
Skill Claude CodeCodex
Domain-validated pipeline guidance for calcium imaging data analysis: motion correction, ROI extraction, neuropil correction, spike inference, and quality control.
Skill Claude CodeCodex
Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.
Skill Claude CodeCodex
Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).
Skill Claude CodeCodex
Domain-validated decision logic for optogenetic stimulation parameter selection, including opsin choice, light delivery, pulse protocols, fiber placement, and control conditions.
Skill Claude CodeCodex
Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.
Skill Claude CodeCodex
Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand…
Skill Claude CodeCodex
Advises on lesion-symptom mapping methods: VLSM, disconnection analysis, network lesion mapping.
Skill Claude CodeCodex
Domain-validated decision logic for selecting neuropsychological test batteries matched to suspected cognitive deficit profiles.
Skill Claude CodeCodex
Designs habituation and preferential-looking paradigms with age-appropriate timing parameters and exclusion criteria.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: