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Claude Skills by NVlabs
github.com/NVlabs1,342 skills6 installs400 views
- Alterlab ClinicaltrialsQuery ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase and retrieve trial details by NCT ID. Use when finding interventional or observational studies, checking trial status and eligibility for patient matching, or exporting clinical trial records for research. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab ClinpgxAccess ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/som...Votes: 0GitHub stars: 36
- Alterlab ClinvarQuery NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies b...Votes: 0GitHub stars: 36
- Alterlab DaskScales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed task graphs, and cluster execution. Use when existing pandas/NumPy code must run on larger-than-RAM data or across clusters, for parallel file processing, distributed ML, or integration with existing pandas code. For out-of-core analytics on a single machine prefer vaex; for in-memory speed prefer polars. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab DatamolWraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel batch processing, returning native rdkit.Chem.Mol objects. Use when running standard cheminformatics pipelines on molecule tables with minimal boilerplate; for low-level control, custom sanitization, or specialized a...Votes: 0GitHub stars: 36
- Alterlab DeepchemRuns molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use when running end-to-end molecular ML experiments that need MoleculeNet benchmarks, scaffold splitting, or ready-made models with minimal setup; for building custom PyTorch graph architectures prefer alterlab-torchdrug, and for standalone mo...Votes: 0GitHub stars: 36
- Alterlab DeeptoolsProcess and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/peak heatmaps and profiles (computeMatrix, plotHeatmap, plotProfile). Use for coverage tracks, signal heatmaps/profiles, normalization (RPGC/CPM/RPKM), and effective-genome-size lookups for ChIP-seq, ATAC-seq, MNase-se...Votes: 0GitHub stars: 36
- Alterlab Digital HumanitiesApplies computational methods to humanities research — text mining and NLP (LDA/BERTopic topic modeling, sentiment, named entity recognition with spaCy/NLTK), corpus linguistics (concordance, collocation, keyness), digital archives (Dublin Core, TEI XML), GIS for history, network analysis, stylometry and authorship attribution, OCR (Tesseract, Kraken, Transkribus), and data visualization (Gephi, Palladio). Use when distant-reading a literary corpus, mapping historical events or trade networks...Votes: 0GitHub stars: 36
- Alterlab EdaExploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/statistics checks, and writes a markdown EDA report with downstream recommendations. Use when asked to "explore", "analyze", "summarize", "profile", or "QC" a data file, or to understand its structure/content/quality before deciding what analysis to run. Covers tabular (.csv .tsv .xlsx .parquet), arrays (.npy .npz .hdf5 .h5 .mat .fits), sequence/genomics (.fasta .fastq .sam .bam .vcf .b...Votes: 0GitHub stars: 36
- Alterlab EdgartoolsAccesses, analyzes, and extracts data from SEC EDGAR filings using the edgartools Python library. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SEC regulatory filings. Part of...Votes: 0GitHub stars: 36
- Alterlab EnaAccess the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab EnsemblQuery the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab EsmRun ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, and function, and ESM C for efficient embeddings and representations — locally or via the cloud Forge API. Use when working with protein sequences, structures, or function prediction, designing novel proteins, generating protein embeddings, performing inverse folding, or doing protein-engineering tasks. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab FlowioParse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting channels and metadata, or preprocessing cytometry data for downstream gating and analysis. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab Genai Camera DirectorThis skill should be used when the user asks about "camera moves", "AI camera presets", "dolly", "crane shot", "orbit shot", "crash zoom", "bullet time", "360 orbit", "FPV arc", "pan", "tilt", "dutch angle", "tracking shot", "Higgsfield camera", "Cinema Studio", "camera direction", "cinematic grammar", "Sora 2 Presets", "Higgsfield Assist", "Soul Cast", "content scoring", "act as a camera director", "camera director mode", "camera language", "lens selection", "focal length", "21:9 cinematic",...Votes: 0GitHub stars: 36
- Alterlab Genai Image To VideoThis skill should be used when the user asks about "image-to-video", "still to motion", "animate my image", "Higgsfield video", "Soul Cinema Preview", "Seedance 1.5 Pro", "AI video generation", "Sora 2", "Kling 2.6", "Kling 3.0", "Veo 3.1", "Wan 2.6", "MiniMax Hailuo 02", "Higgsfield Assist", "Soul Cast", "content scoring", "act as an image-to-video director", "image-to-video mode", "camera motion on stills", "dolly on image", "Soul ID video", "character consistency in video", "upscale video"...Votes: 0GitHub stars: 36
- Alterlab Genai Motion DesignerThis skill should be used when the user asks about "AI motion design", "Higgsfield effects", "AI VFX", "style transfer video", "Ghibli anime style", "watercolor animation", "draw to video", "sketch animation", "Soul Inpaint", "Kling Video Edit", "AI video transitions", "video effects layering", "motion pacing", "act as a motion designer", "motion designer mode", "AI video compositing", "Canvas workspace", "batch video generation", "video style consistency", "multi-shot sequencing", "social me...Votes: 0GitHub stars: 36
- Alterlab Genai Music ProducerThis skill should be used when the user asks about "AI music", "Suno", "song creation", "music generation", "lyrics writing", "song structure", "verse chorus bridge", "genre prompting", "lo-fi", "cinematic music", "indie folk", "electronic music", "hip hop beat", "song extending", "stems separation", "music for social media", "act as a music producer", "music producer mode", "AI song", "custom lyrics", "song variations", "remix style", "music prompt", "MIDI export", "negative prompt", "sectio...Votes: 0GitHub stars: 36
- Alterlab Genai Soundtrack ComposerThis skill should be used when the user asks about "soundtrack", "film scoring", "background music", "scene music", "mood music", "instrumental generation", "content scoring", "video music", "podcast music", "ambient music", "transition music", "stinger", "musical identity", "music licensing", "soundtrack library", "act as a soundtrack composer", "soundtrack composer mode", "score a scene", "music for video", "emotional music", "cinematic score", "Suno instrumental", "MIDI export for scoring"...Votes: 0GitHub stars: 36
- Alterlab Genai Talking HeadThis skill should be used when the user asks about "AI talking head", "UGC builder", "Higgsfield Speak 2.0", "lipsync video", "Lipsync Studio", "selfie to video", "Kling Lipsync", "Kling Speak", "Sync.so", "Higgsfield Assist", "Soul Cast", "content scoring", "digital presenter", "AI spokesperson", "synthetic presenter", "talking avatar", "lip sync", "AI testimonial video", "act as a talking head creator", "talking head mode", "Veo 3 UGC", "photo to talking video", "AI voiceover video", "expre...Votes: 0GitHub stars: 36
- Alterlab Gene DbQuery NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab GenimlMachine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomization, and BBClient/BEDbase caching. Use when training or using region/cell embeddings, clustering scATAC-seq, building a tokenization universe from BED collections, or any ML/feature-learning task o...Votes: 0GitHub stars: 36
- Alterlab GeomasterCovers geospatial science across remote sensing, GIS, spatial analysis, and machine learning for earth observation — satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), raster and DEM operations, spectral indices (NDVI/EVI/NDWI), spatial statistics, point cloud processing, network analysis, and cloud-native workflows (STAC, COG, Planetary Computer), with examples across Python, R, Julia, JavaScript, C++, Java, Go, and Rust. Use for remote sensing workflows, satellite/...Votes: 0GitHub stars: 36
- Alterlab GeopandasReads, writes, and analyzes geospatial vector data with the GeoPandas Python library (shapefiles, GeoJSON, GeoPackage), with PostGIS support and integration with matplotlib, folium, and cartopy. Use for spatial analysis and geometric operations — buffer analysis, spatial joins and overlays between datasets, dissolving boundaries, clipping, calculating areas and distances, reprojecting coordinate systems, choropleth mapping, or converting between vector file formats. This is for tabular vector...Votes: 0GitHub stars: 36
- Alterlab GgetRun fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for multi-database Python workflows use bioservices. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab GlycoengineeringAnalyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing therapeutic-antibody or biologic glycoforms, or doing glycoprotein engineering and vaccine-design work. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab GtarsRuns high-performance genomic interval analysis with gtars (databio), a Rust toolkit with Python bindings — the performance-critical backend for the geniml ML library. Use when computing overlaps/jaccard/coverage between BED region sets, indexing intervals with IGD, generating uniwig accumulation/coverage tracks, tokenizing genomic regions for ML, splitting single-cell fragments into pseudobulks, or computing GA4GH refget sequence digests. NOT for training region embeddings (use alterlab-geni...Votes: 0GitHub stars: 36
- Alterlab GwasQuery the NHGRI-EBI GWAS Catalog REST API for SNP-trait associations, retrieving variants by rs ID, disease/trait, or gene along with p-values and summary statistics. Use when investigating genome-wide association study hits, mapping a SNP or rsID to traits, building polygenic risk scores, or doing genetic epidemiology lookups. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab Hedgefund MonitorQueries the OFR (Office of Financial Research) Hedge Fund Monitor API for time series on hedge fund size, leverage, counterparties, liquidity, complexity, and risk management, including SEC Form PF aggregated statistics, CFTC Traders in Financial Futures, FICC Sponsored Repo volumes, and FRB SCOOS dealer financing terms (no API key or registration required). Use when working with hedge fund data, systemic risk monitoring, financial stability research, hedge fund leverage or leverage ratios, c...Votes: 0GitHub stars: 36
- Alterlab HmdbAccess the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve chemical properties, biomarker data, NMR/MS reference spectra, and associated pathways. Use when identifying a human metabolite, looking up its biomarker or disease associations, matching NMR/MS spectra, or running metabolomics annotation. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab Hypothesis GenFormulates structured, testable hypotheses from experimental observations using a scientific-method framework — derives predictions, proposes mechanisms, and designs experiments to test them, then renders a LaTeX report. Use when turning observations or data into falsifiable, mechanistic hypotheses, competing-explanation sets, testable predictions, or experimental designs. For a standalone systematic literature review or evidence synthesis (not a means to hypotheses) use alterlab-literature-r...Votes: 0GitHub stars: 36
- Alterlab Imaging Data CommonsQuery and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python package, filtering by metadata, visualizing in-browser, and checking licenses, with no authentication required. Use when obtaining large-scale radiology (CT, MR, PET) or digital pathology DICOM datasets for AI/ML training or cancer imaging research. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab Iso13485Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a documentation gap analysis, drafting a Quality Manual or SOP/work instruction, assembling a Medical Device File, identifying missing documentation for medical device certification, or when medical device regulations, QMS...Votes: 0GitHub stars: 36
- Alterlab KeggProvide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-pathway mapping, metabolic reactions, KEGG Orthology (KO), drug-drug interactions, and ID conversion. Use when querying KEGG pathways, mapping genes/compounds to metabolic maps, or running KEGG pathway enrichment via raw HTTP/REST; for protein-protein interaction networks prefer alterlab-string-db, for protein sequences and annotations prefer alterlab-uniprot, and for Python workfl...Votes: 0GitHub stars: 36
- Alterlab LamindbManage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Ac...Votes: 0GitHub stars: 36
- Alterlab Link HealthAudits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links; designed for lychee-based GitHub Actions link checkers but generalizes to markdown-link-check and similar tools. Use when the request mentions link audit, dead links, link health, lychee, broken links, link checker, ...Votes: 0GitHub stars: 36
- Alterlab Literature ReviewConducts comprehensive, systematic literature reviews across multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar), with PRISMA flow tracking, study screening (title/abstract and full-text), evidence-table extraction, and risk-of-bias assessment, producing professionally formatted markdown documents and PDFs with verified citations in multiple styles (APA, Nature, Vancouver). Use when running a systematic literature review, meta-analysis, research synthesis, or broad literatu...Votes: 0GitHub stars: 36
- Alterlab MatchmsComputes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab MermaidWrites Markdown documents and text-based Mermaid diagrams (flowcharts, sequence, class, ER, gantt, state, and more) with full style guides, 24 diagram-type references, and 9 document templates. Use when authoring a scientific document, report, analysis, or README, or when a diagram should be expressed as version-controllable Mermaid/Markdown text rather than a rendered image. For AI-rendered publication schematics use scientific-schematics instead. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab Metabolomics WbAccess the NIH Metabolomics Workbench via its REST API (4,200+ studies), querying metabolites, RefMet standardized nomenclature, MS/NMR data, m/z mass searches, and study metadata. Use when retrieving public metabolomics study data, standardizing metabolite names with RefMet, running m/z lookups, or doing biomarker discovery. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab Mixed MethodsMixed methods research design and integration strategies for combining qualitative and quantitative approaches. Use when planning convergent, explanatory sequential, exploratory sequential, embedded, transformative, or multiphase designs; when integrating diverse data sources through merging, connecting, or embedding; when constructing joint displays or meta-inferences; or when evaluating quality criteria specific to mixed methods research. Covers Creswell & Plano Clark frameworks, notation s...Votes: 0GitHub stars: 36
- Alterlab Molecular DynamicsRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces). Use when simulating protein or ligand dynamics, equilibrating a system, or computing trajectory metrics for structural biology, drug binding, or biophysics. Part of the AlterLab Academic Skills suite.Votes: 0GitHub stars: 36
- Alterlab MolfeatFeaturizes molecules for machine learning with molfeat (100+ featurizers) — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, GIN) exposed as scikit-learn transformers that convert SMILES into feature vectors. Use when turning molecules into ML-ready feature matrices for QSAR/QSPR or virtual screening, or benchmarking fingerprint against descriptor and embedding representations; for training models and MoleculeNet bench...Votes: 0GitHub stars: 36
- Alterlab NetworkxCreates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing topologies — applicable to social, biological, transportation, citation, and any pairwise-relationship networks. This is classical graph analytics, not deep learning — for train...Votes: 0GitHub stars: 36
- Alterlab Neurokit2Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when computing heart rate variability (HRV), event-related potentials, complexity measures, autonomic nervous system assessment, or multi-modal physiological signal integration for psychophysiology research. Part of the A...Votes: 0GitHub stars: 36
- Alterlab NeuropixelsAnalyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when working with neural recordings, spike sorting, or extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation. Part of the AlterLab Academic S...Votes: 0GitHub stars: 36
- Alterlab Nmc Data JournalistThis skill should be used when the user asks about "data journalism", "data visualization", "data storytelling", "FOIA request", "RTI request", "spreadsheet analysis", "chart design", "act as a data journalist", "data journalist mode", "infographic", "open data", "statistical analysis for journalism", "investigative data", "public records", "Datawrapper", "Flourish", "Tableau Public", "D3.js", "chart type selection", or needs expertise in finding, analyzing, and visualizing data for journalis...Votes: 0GitHub stars: 36
- Alterlab Nmc Digital CampaignThis skill should be used when the user asks about "digital campaign", "social impact campaign", "digital activism", "civic tech", "awareness campaign", "advocacy campaign", "act as a digital campaign planner", "digital campaign mode", "hashtag campaign", "change.org petition", "awareness-to-action funnel", "online mobilization", "cause marketing", "social change campaign", "petition strategy", or needs expertise in designing and executing digital campaigns for social impact and civic engagem...Votes: 0GitHub stars: 36
- Alterlab Nmc Digital EthicsThis skill should be used when the user asks about "digital ethics", "media ethics", "AI ethics", "platform governance", "misinformation", "disinformation analysis", "act as a digital ethics advisor", "digital ethics mode", "algorithmic bias", "data privacy", "content moderation", "ethical framework", "deepfake", "surveillance", "fact-checking tools", "verification workflow", "platform audit", "ethics stress test", "algorithmic accountability", "informed consent", "digital rights", "tech regu...Votes: 0GitHub stars: 36
- Alterlab Nmc Media TheoryThis skill should be used when the user asks about "media theory", "critical theory", "academic writing", "Foucault", "Habermas", "McLuhan", "Baudrillard", "Stuart Hall", "act as a media theory companion", "media theory mode", "theoretical framework", "literature review", "discourse analysis", "semiotics", "cultural studies", "political economy", or needs expertise in applying media and communication theory to academic writing and critical analysis. Part of the AlterLab FC Skills collection (...Votes: 0GitHub stars: 36