neuroaihub
- 61 skills
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- ▌ Alphagenome Single Variant Analysis · neuroaihub bundleAnalyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.
- ▌ Uv · neuroaihubChecks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH. Use when another skill requires uv as a prerequisite.
- ▌ Audit Evidence · neuroaihub bundleAudit numeric, artifact, log, citation, and cross-report claims against inspectable evidence. Use for reports, syntheses, benchmark claims, external citations, or conflicting Expert outputs.
- ▌ Curate Research Trace · neuroaihub bundleCurate BrainPilot Trace Events into human-readable research Episodes, appropriately granular nodes, and direct depends_on relationships. Use when a report contains multiple settings, results, analyses, visualizations, findings, or conclusions; when Episode placement is unclear; or when deciding whether new evidence should create parallel/sequential nodes or update an existing node.
- ▌ Audit Code Artifact · neuroaihub bundleAudit scientific implementation, exported-model equivalence, dependency completeness, manifests, packaging, and isolated inference. Use when claims depend on code, trained artifacts, evaluators, or deployable entry points.
- ▌ Audit Feedback Loop · neuroaihub bundleCoordinate iterative evidence and reliability reviews between BrainPilot's Principal Investigator and Auditor. Use when PI needs to audit its own draft, an Expert result, or a multi-agent synthesis; when Auditor receives such a review task; or when a previous audit requires correction and incremental re-review.
- ▌ Audit Data Integrity · neuroaihub bundleAudit scientific data semantics, sample and label alignment, leakage, group splits, preprocessing boundaries, and train-to-inference transforms. Use for any result based on datasets, feature matrices, tensors, repeated observations, or learned preprocessing.
- ▌ Audit Model Validation · neuroaihub bundleAudit whether method discovery, comparison, representative real-data validation, collapse diagnostics, pruning, and selection evidence support claims of suitability or superiority. Use for research-method selection, empirical evaluation, benchmarking, modelling, prediction, or other conclusions that depend on choosing among alternatives.
- ▌ Create Data Inventory · neuroaihub bundleCreate or update the canonical Markdown inventory of task-relevant research data. Engineer must invoke this skill before creating or updating any data inventory, data contract, or dataset-coverage summary that downstream agents will use.
- ▌ Opentargets Database · neuroaihub bundleQuery Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
- ▌ Source Grounded Research Report · neuroaihubResearch a bounded factual, documentation, API, or literature question from authoritative sources and save a self-contained Markdown report with claim-level citations. Use for reading-heavy evidence gathering, not experiment execution or data analysis.
- ▌ Fmriprep · neuroaihub bundlePreprocess 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, choose output spaces (MNI152NLin2009cAsym, fsaverage, fsLR/CIFTI), configure susceptibility distortion correction (SDC), extract or interpret the confounds table, resample to surface/grayordinates, cite fMRIPrep and its dependencies, or debug fMRIPrep crashes and hangs.
- ▌ Deeplabcut · neuroaihub bundleToolbox for markerless animal pose estimation with DeepLabCut. Covers single/multi-animal tracking, SuperAnimal pretrained models, 2D/3D pose estimation, keypoint labeling GUI, model training/evaluation, video analysis, and behavioral quantification. Use when the user needs animal pose estimation, behavior tracking, keypoint detection in videos, or mentions DeepLabCut/DLC/SuperAnimal.
- ▌ Share Case · neuroaihubOne-command community case sharing — capture research context from your session and submit to GitHub Discussions
- ▌ Share Usage · neuroaihub bundleGenerate and share anonymized skill usage statistics to help the community understand which skills are most valuable
- ▌ Erp Analysis · neuroaihub bundleDomain-validated pipeline and parameter guidance for event-related potential analysis, from preprocessing through statistical testing
- ▌ Verify Skill · neuroaihubInteractive skill verification — assess accuracy of parameters, citations, and methodology through structured expert review
- ▌ Repo To Skill · neuroaihubConvert a GitHub repository or local codebase into a well-structured Claude Code skill with progressive disclosure. Use this skill whenever the user provides a GitHub URL or local repo path and asks to turn it into a skill, create a skill from a repo, or convert a library/tool/framework into reusable skill documentation. Also trigger when users say things like 'make a skill from this repo', 'turn this codebase into a skill', or 'I want a skill for [library name]'.
- ▌ Paper To Skill · neuroaihub bundleInteractive skill that guides extraction of research paradigms and methodological techniques from cognitive science papers into structured, reusable skills
- ▌ Pycortex Guide · neuroaihub bundleDomain-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 whenever the user mentions pycortex, `import cortex`, cortical surfaces, brain flatmaps, WebGL brain viewers, cortical surface mapping, or wants to visualize neuroimaging data on the cortex, even if they don't explicitly name pycortex.
- ▌ Contribute Skill · neuroaihubOne-command skill contribution — generate a SKILL.md from your domain expertise and submit to GitHub Issues for maintainer review
- ▌ Mne Python Guide · neuroaihub bundleDomain-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 user works with EEG/MEG/sEEG/ECoG/NIRS/eye-tracking data in Python, mentions MNE, or needs neurophysiological analysis guidance.
- ▌ Cogsci Statistics · neuroaihub bundleDomain-specific statistical modeling guidance for cognitive science and neuroscience, encoding when and how to apply mixed models, correction methods, Bayesian approaches, and effect size reporting
- ▌ Research Literacy · neuroaihub bundleCore scientific methodology principles: research planning, method justification, assumption checking, and human-in-the-loop decision making for cognitive science and neuroscience
- ▌ Tom Task Selector · neuroaihub bundleSelects Theory of Mind tasks matched to target population, age, and construct with psychometric guidance
- ▌ Act R Model Builder · neuroaihub bundleGuides ACT-R cognitive model construction: chunk types, production rules, subsymbolic parameters, and model validation
- ▌ Netneurotools Guide · neuroaihub bundleDomain-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 on brain networks, parcellated brain data (Schaefer, Cammoun, Desikan-Killiany), cortical surface templates (fsaverage, fsLR, CIVET, Conte69), network communication metrics, null model generation, spatial autocorrelation on brain maps, community detection in connectomes, or surface-based visualization with PyVista/PySurfer. Also trigger when the user mentions netneurotools, netneurolab, structure-function coupling, network neuroscience, brain graph analysis, or needs to fetch neuroimaging atlases and templates.
- ▌ Cogsci Visualization · neuroaihub bundleDomain-specific visualization best practices for cognitive and neuroscience data, encoding plot type selection, color standards, and publication formatting
- ▌ Spikeinterface Skill · neuroaihub bundleDomain knowledge for building extracellular electrophysiology pipelines with SpikeInterface: loading data with extractors, preprocessing, running spike sorters, post-processing via SortingAnalyzer, quality metrics, curation, comparison, visualization, and export.
- ▌ Cogsci Power Analysis · neuroaihub bundleDomain-specific statistical power analysis guidance for cognitive and neuroscience research, encoding effect size priors and sample size recommendations by modality
- ▌ Drift Diffusion Model · neuroaihub bundleExpert guidance on selecting, fitting, and evaluating drift-diffusion models for two-choice response time data in cognitive science
- ▌ Eeg Paradigm Designer · neuroaihub bundleExpert guidance for designing EEG paradigms optimized to isolate specific ERP components, with domain-validated timing, trial count, and control condition parameters
- ▌ Reading Time Analysis · neuroaihub bundleGuides analysis of eye-tracking reading measures including first fixation, gaze duration, regression path, and total reading time
- ▌ Fmri Task Design Guide · neuroaihub bundleGuides fMRI task design: block vs. event-related vs. mixed; jittering; contrasts; power for BOLD detection
- ▌ Fmri Glm Analysis Guide · neuroaihub bundleDomain-validated guidance for fMRI General Linear Model specification: HRF modeling, design matrix construction, contrast definition, confound regression, and statistical inference
- ▌ Markdown Report Writing · neuroaihub bundleGuide AI agents to write beautifully formatted, well-illustrated Markdown reports with proper structure, diagrams, and compatibility across GitHub and Obsidian. Use this skill whenever the user asks you to write a report, project documentation, experiment report, README, technical document, or any long-form Markdown content. Also trigger when users mention Markdown formatting, Mermaid diagrams, report templates, or document publishing.
- ▌ Contribute Skills Via Pr · neuroaihubStep-by-step guidance for contributing a new skill to the NeuroAIHub/awesome_cognitive_and_neuroscience_skills repository via GitHub Pull Request, including SKILL.md format requirements, quality rules, and PR checklist
- ▌ Neural Decoding Analysis · neuroaihub bundleDomain-validated methods and decision logic for neural decoding, RSA, temporal generalization, and encoding models in systems neuroscience
- ▌ Neuroimaging Power Guide · neuroaihub bundleSample-size planning for fMRI/EEG studies using effect-size benchmarks and simulation-based power
- ▌ Cognitive Paradigm Design · neuroaihub bundleExpert guidance for selecting and parameterizing cognitive psychology experimental paradigms based on research questions
- ▌ Sentence Stimulus Norming · neuroaihub bundleSpecifies norming procedures for linguistic stimuli including cloze probability, plausibility ratings, acceptability judgments, and lexical controls
- ▌ Signal Detection Analysis · neuroaihub bundleDomain-validated decision logic, formulas, and interpretation guidelines for applying Signal Detection Theory to cognitive science data
- ▌ Brain Connectivity Modeler · neuroaihub bundleAdvises on functional/effective connectivity methods: PPI, DCM, Granger causality, graph theory
- ▌ Divergent Thinking Scoring · neuroaihub bundleDomain-validated multi-dimensional scoring system for divergent thinking tasks, including fluency, flexibility, originality, and automated semantic distance methods
- ▌ Parameter Recovery Checker · neuroaihub bundleGuides parameter recovery studies to validate model identifiability before trusting fitted parameter values
- ▌ Neuropsych Battery Selector · neuroaihub bundleDomain-validated decision logic for selecting neuropsychological test batteries matched to suspected cognitive deficit profiles
- ▌ Self Paced Reading Designer · neuroaihub bundleExpert guidance for designing self-paced reading experiments: region segmentation, timing parameters, comprehension probes, and spillover analysis
- ▌ Infant Looking Time Designer · neuroaihub bundleDesigns habituation and preferential-looking paradigms with age-appropriate timing parameters and exclusion criteria
- ▌ Lesion Symptom Mapping Guide · neuroaihub bundleAdvises on lesion-symptom mapping methods: VLSM, disconnection analysis, network lesion mapping
- ▌ Spiking Network Model Builder · neuroaihub bundleAssists building spiking neural network simulations: neuron models, connectivity, plasticity rules
- ▌ Visual Search Array Generator · neuroaihub bundleSpecifies display parameters, set sizes, target-distractor similarity, and randomization constraints for visual search experiments
- ▌ Alternative Uses Task Designer · neuroaihub bundleDomain-validated guidance for designing Alternative Uses Task (AUT) experiments measuring divergent thinking, with parameters for AI-augmented and traditional conditions
- ▌ Calcium Imaging Analysis Guide · neuroaihub bundleDomain-validated pipeline guidance for calcium imaging data analysis: motion correction, ROI extraction, neuropil correction, spike inference, and quality control
- ▌ Evidence Accumulation Selector · neuroaihub bundleAdvises on when to use DDM vs. LBA vs. race models for choice-RT data based on experimental design and research goals
- ▌ Optogenetics Protocol Designer · neuroaihub bundleDomain-validated decision logic for optogenetic stimulation parameter selection, including opsin choice, light delivery, pulse protocols, fiber placement, and control conditions
- ▌ Bayesian Cognitive Model Builder · neuroaihub bundleDomain-validated guidance for building hierarchical Bayesian cognitive models with Stan/PyMC: prior specification, model structure, MCMC diagnostics, and posterior predictive checks
- ▌ Eeg Preprocessing Pipeline Guide · neuroaihub bundleGuides EEG preprocessing: filtering, artifact rejection (ICA/ASR), re-referencing, interpolation
- ▌ Neural Population Analysis Guide · neuroaihub bundleGuides dimensionality reduction and latent-variable analysis of neural populations (PCA, GPFA, dPCA)
- ▌ Fmri Preprocessing Pipeline Guide · neuroaihub bundleDomain-validated guidance for fMRI preprocessing decisions: motion correction, slice timing, spatial normalization, smoothing, confound regression, and quality control
- ▌ Creativity Self Efficacy Mediation · neuroaihub bundleDomain-validated guidance for SEM-based mediation analysis of creative self-efficacy and moderation by baseline creativity in AI-augmented creativity research
- ▌ Neuroimaging Sample Size Calculator · neuroaihub bundleSimulation-based sample-size planning for neuroimaging studies using effect-size maps