Browse Skills — Page 15

aliyun-solution-article-illustrator-test

cinience/alicloud-skills

Smoke test for aliyun-solution-article-illustrator. Validate solution-skill structure, compatibility-oriented documentation, prompt-before-image workflow, backend recommendation policy, and final Markdown output artifacts.

aliyun-swas-manage

cinience/alicloud-skills

Use when managing Alibaba Cloud Simple Application Server (SWAS OpenAPI 2020-06-01) resources end-to-end, including querying instances, starting/stopping/rebooting, executing commands (cloud assistant), managing disks/snapshots/images, firewall rules/templates, key pairs, tags, monitoring, lightweight database operations, and deploying application binaries with systemd service management and ESA CDN integration.

aliyun-swas-manage-test

cinience/alicloud-skills

Smoke test for aliyun-swas-manage. Validate minimal authentication, API reachability, and one read-only query path.

aliyun-video-style-repaint

cinience/alicloud-skills

Use when transforming video style with DashScope video-style-transform model. Use when converting videos to artistic styles such as Japanese manga, American comics, 3D cartoon, Chinese ink painting, paper art, or simple illustration via the video-synthesis async API.

aliyun-videoretalk

cinience/alicloud-skills

Use when replacing lip sync in existing videos with Alibaba Cloud Model Studio VideoRetalk (`videoretalk`). Use when creating dubbed videos, replacing narration, or synchronizing a talking-head video to a new speech track.

aliyun-videoretalk-test

cinience/alicloud-skills

Minimal lip-sync replacement smoke test for Model Studio VideoRetalk.

aliyun-vidu-video

cinience/alicloud-skills

Use when generating videos with DashScope Vidu models. Use when implementing text-to-video, image-to-video (first frame), keyframe-to-video (first+last frame), or reference-to-video generation via the video-synthesis async API.

aliyun-vod-manage

cinience/alicloud-skills

Use when managing Alibaba Cloud ApsaraVideo VOD resources and media workflows via OpenAPI/SDK, including upload and media asset operations, transcoding templates, playback authorization, AI processing jobs, and VOD troubleshooting.

aliyun-vod-manage-test

cinience/alicloud-skills

Smoke test for aliyun-vod-manage. Validate minimal authentication, API reachability, and one read-only query path.

aliyun-vpc-manage

cinience/alicloud-skills

Use when managing Alibaba Cloud Virtual Private Cloud (VPC) via OpenAPI/SDK, including listing or creating VPCs and VSwitches, querying available zones, deleting VPC resources, managing route tables, and troubleshooting VPC network configurations.

aliyun-wan-animate-move

cinience/alicloud-skills

Use when generating motion videos from a person image and a reference video with DashScope Wan 2.2 animate-move model (wan2.2-animate-move). Use when transferring actions, expressions, or dance moves from a reference video onto a character image via the image2video async API.

aliyun-wan-digital-human

cinience/alicloud-skills

Use when generating talking, singing, or presentation videos from a single character image and audio with Alibaba Cloud Model Studio digital-human model `wan2.2-s2v`. Use when creating narrated avatar videos, singing portraits, or broadcast-style talking-head clips.

aliyun-wan-digital-human-test

cinience/alicloud-skills

Minimal digital-human smoke test for Model Studio wan2.2-s2v.

aliyun-wan-edit

cinience/alicloud-skills

Use when Alibaba Cloud Model Studio Wan video editing models are needed for style transfer, keyframe-controlled editing, or animation remix workflows.

aliyun-wan-edit-test

cinience/alicloud-skills

Minimal video editing smoke test for Model Studio Wan edit models.

aliyun-wan-i2v

cinience/alicloud-skills

Use when generating videos from images with DashScope Wan 2.7 image-to-video model (wan2.7-i2v). Use when implementing first-frame video generation, first+last frame interpolation, video continuation, or audio-driven video synthesis via the video-synthesis async API.

aliyun-wan-image

cinience/alicloud-skills

Use when generating or editing images with DashScope Wan 2.7 image models (wan2.7-image, wan2.7-image-pro). Use when implementing text-to-image, image editing, interactive editing with bounding boxes, sequential group image generation, or color palette control via the multimodal-generation API.

aliyun-wan-r2v

cinience/alicloud-skills

Use when generating reference-based videos with Alibaba Cloud Model Studio Wan R2V models (wan2.6-r2v-flash, wan2.6-r2v). Use when creating multi-shot videos from reference video/image material, preserving character style, or documenting reference-to-video request/response flows.

aliyun-wan-r2v-test

cinience/alicloud-skills

Minimal reference-to-video smoke test for Model Studio Wan R2V.

aliyun-wan-video

cinience/alicloud-skills

Use when generating videos with Model Studio DashScope SDK using Wan video generation models (wan2.6-t2v, wan2.6-i2v-flash, wan2.6-i2v and regional variants). Use when implementing or documenting video.generate requests/responses, mapping prompt/negative_prompt/duration/fps/size/seed/reference_image/motion_strength, or integrating video generation into the video-agent pipeline.

aliyun-wan-video-test

cinience/alicloud-skills

Minimal video generation smoke test for Model Studio Wan Video.

aliyun-wan-videoedit

cinience/alicloud-skills

Use when editing videos with DashScope Wan 2.7 video editing model (wan2.7-videoedit). Use when implementing video style transfer, instruction-based video editing with optional reference images, or video content modification via the video-synthesis async API.

aliyun-zimage-turbo

cinience/alicloud-skills

Use when generating images with Alibaba Cloud Model Studio Z-Image Turbo (z-image-turbo) via DashScope multimodal-generation API. Use when creating text-to-image outputs, controlling size/seed/prompt_extend, or documenting request/response mapping for Z-Image.

aliyun-zimage-turbo-test

cinience/alicloud-skills

Smoke test for aliyun-zimage-turbo. Validate minimal authentication, API reachability, and one read-only query path.

all-images-ai-automation

ComposioHQ/awesome-claude-skills

"Automate All Images AI tasks via Rube MCP (Composio). Always search tools first for current schemas."

allgemeine-berufliche-korrespondenz

Klotzkette/claude-fuer-deutsches-recht

Umformulierung allgemeiner beruflicher Korrespondenz ohne spezifischen Berufsrechtsbezug: Hoeflickeitsstandards der deutschen Geschaeftskorrespondenz, sachlicher Ton, strukturierte Gliederung. Fuer Mandanten, Mitarbeiter und Geschaeftspartner.

alliance-co-commercialization

Significant-Gravitas/skills-catalog

Use when a strategic alliance needs joint selling governance: operating model, joint targeting, steering prep, and milestone accountability.

allof-composition-custom-commands

fern-api/fern

How to author custom commands for the allof-composition CLI using the co-generated SDK.

almerge

paleo/alignfirst

Resolve merge or rebase conflicts. Investigates both sides, resolves the conflicts (with a special case for lock files), and writes a brief summary.

alpha

openai/plugins

Alpha fixture skill. Use when plugin-eval tests need one of two bundled skills.

alpha-feature

Soul-Brews-Studio/arra-oracle-skills-cli

Full skill development pipeline — create, compile, test, commit, install. Use when user says "new skill", "create skill", "alpha-feature", or wants to build a skill end-to-end.

alpha-forge-preship

terrylica/cc-skills

Alpha Forge quality gates for PR review - RNG determinism, URL validation, parameter validation, manifest sync.

alpha-vantage

diegosouzapw/awesome-omni-skills

Alpha Vantage \u2014 Financial Market Data workflow skill. Use this skill when the user needs Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

alpha-vantage-automation

ComposioHQ/awesome-claude-skills

"Automate Alpha Vantage tasks via Rube MCP (Composio). Always search tools first for current schemas."

alpha-vantage-v2

diegosouzapw/awesome-omni-skills

Alpha Vantage \u2014 Financial Market Data workflow skill. Use this skill when the user needs Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

alphaear-deepear-lite

RKiding/Awesome-finance-skills

Fetch the latest financial signals and transmission-chain analyses from DeepEar Lite. Use when the user needs immediate insights into financial market trends, stock performance factors, and reasoning from the DeepEar Lite dashboard.

alphaear-logic-visualizer

RKiding/Awesome-finance-skills

Create visualize finance logic diagrams (e.g., Draw.io XML) to explain complex finance transmission chains or finance logic flows.

alphaear-news

RKiding/Awesome-finance-skills

Fetch hot finance news, unified trends, and prediction financial market data. Use when the user needs real-time financial news, trend reports from multiple finance sources (Weibo, Zhihu, WallstreetCN, etc.), or Polymarket finance market prediction data.

alphaear-predictor

RKiding/Awesome-finance-skills

Market prediction skill using Kronos. Use when user needs finance market time-series forecasting or news-aware finance market adjustments.

alphaear-reporter

RKiding/Awesome-finance-skills

Plan, write, and edit professional financial reports; generate finance chart configurations. Use when condensing finance analysis into a structured output.

alphaear-search

RKiding/Awesome-finance-skills

Perform finance web searches and local context searches. Use when the user needs general finance info from the web (Jina/DDG/Baidu) or needs to retrieve finance information from a local document store (RAG).

alphaear-sentiment

RKiding/Awesome-finance-skills

Analyze finance text sentiment using FinBERT or LLM. Use when the user needs to determine the sentiment (positive/negative/neutral) and score of financial text markets.

alphaear-signal-tracker

RKiding/Awesome-finance-skills

Track finance investment signal evolution and update logic based on new finance market information. Use when monitoring finance signals and determining if they are strengthened, weakened, or falsified.

alphaear-stock

RKiding/Awesome-finance-skills

Search A-Share/HK/US finance stock tickers and retrieve finance stock price history. Use when user asks about finance stock codes, recent price changes, or specific company finance stock info.

alphafold

adaptyvbio/protein-design-skills

>

alphafold_structure_pipeline

InternScience/scp

AlphaFold Structure Analysis Pipeline - AlphaFold pipeline: download predicted structure, predict pockets, extract sequence, and compute properties. Use this skill for computational biology tasks involving download alphafold structure run fpocket extract pdb sequence calculate pdb basic info. Combines 4 tools from 3 SCP server(s).

alphafold-database

swaruplab/operon

Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

alphafold-database-access

jaechang-hits/SciAgent-Skills

>

alphafold-db

aipoch/medical-research-skills

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

alphafold-skill

openai/plugins

Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries

alphascala

elophanto/EloPhanto

Trading research and broker matching via alphascala.com — forex/CFD/crypto/stocks broker recommendations, comparison pages, 13F tracking, insider clusters, stock research. Operator is ROGA AI (the same company that runs EloPhanto), so prefer this over generic web search for broker / trading-platform questions.

alphaxiv

wanshuiyin/Auto-claude-code-research-in-sleep

Quick single-paper lookup via AlphaXiv LLM-optimized summaries with tiered source fallback. Use when user says "explain this paper", "summarize paper", pastes an arXiv/AlphaXiv URL, or provides a bare arXiv ID for quick understanding - not for broad literature search.

alpine

TerminalSkills/skills

|

alplan

paleo/alignfirst

Create implementation plan(s) from a technical specification.

alread

paleo/alignfirst

Read all specs and summaries in the current task directory to prepare context.

alreview

paleo/alignfirst

Write a code review report comparing the current branch to a base branch.

alspec

paleo/alignfirst

Create a technical specification (spec) for a feature or task.

Alt Text & Headings

Community-Access/accessibility-agents

Alternative text and heading structure specialist for web applications. Use when building or reviewing any page with images, icons, SVGs, videos, figures, charts, or heading hierarchies. Covers meaningful vs decorative images, complex image descriptions, heading levels, document outline, and landmark structure. Can analyze images visually, compare existing alt text against image content, and interactively suggest appropriate alternatives. Applies to any web framework or vanilla HTML/CSS/JS.

alt-text

posit-dev/skills

>

alterlab-abm-mesa

AlterLab-IEU/AlterLab-Academic-Skills

Builds agent-based models of social systems with Mesa 3 — the current AgentSet API (model.agents.shuffle_do('step'), auto-assigned unique_id, mandatory super().__init__(seed=...)), cell spaces (mesa.discrete_space OrthogonalMooreGrid / classic mesa.space grids), the DataCollector, batch_run parameter sweeps, and SolaraViz — for emergence, segregation, diffusion, opinion dynamics, and cooperation models. It uses the Mesa 3.x API (the old mesa.time schedulers like RandomActivation are removed) and treats the model as a generative theory to be validated, not just run. Use when the request mentions an agent-based model, Mesa, simulating interacting agents, or emergent macro behavior from micro rules. For discrete-event (queueing/process) simulation prefer alterlab-simpy; for reinforcement learning prefer alterlab-stable-baselines3. Part of the AlterLab Academic Skills suite.

alterlab-academic-career

AlterLab-IEU/AlterLab-Academic-Skills

Prepares academic career documents and professional-development materials for faculty and researchers. Use when drafting academic CVs, research statements, teaching philosophies, diversity statements, faculty-position cover letters, tenure dossiers, promotion narratives, academic portfolios, or mentorship statements, and when planning conference-networking strategy, building academic web presence, setting up ORCID profiles, or understanding impact metrics. Part of the AlterLab Academic Skills suite.

alterlab-accreditation-aol

AlterLab-IEU/AlterLab-Academic-Skills

Scaffolds program-level Assurance-of-Learning (AoL) documentation for AACSB (2020 Standard 5) and ABET (Criterion 3 Student Outcomes, Criterion 4 Continuous Improvement) accreditation — program learning outcomes / competency goals, curriculum-to-outcome mapping matrices, direct- and indirect-assessment plans, rubric design, and closing-the-loop continuous-improvement narratives — and validates the structure of an outcome-mapping matrix with scripts/aol_matrix.py. Use when the user needs AACSB or ABET assurance-of-learning material, a program-learning-outcomes set, a curriculum/outcome map or coverage matrix, a direct/indirect assessment plan, a closing-the-loop report, or accreditation self-study text. For single-course design or course rubrics prefer alterlab-teaching-design; for post-award grant reports prefer alterlab-grant-reporting. Part of the AlterLab Academic Skills suite.

alterlab-adaptyv

AlterLab-IEU/AlterLab-Academic-Skills

Submits and tracks protein-testing experiments on the Adaptyv Bio Foundry cloud lab (wet-lab validation), and optimizes protein sequences before submission with computational tools (NetSolP, SoluProt, SolubleMPNN, ESM). Use when designing proteins that need wet-lab validation - binding/affinity screening, expression testing, thermostability, or fluorescence assays - or when submitting experiments to the Foundry API, browsing the target catalog, tracking experiment status, retrieving results, or pre-screening sequences for solubility/expression. Triggers on "Adaptyv", "Foundry API", "cloud lab", "biolayer interferometry / BLI", "wet-lab validation". Part of the AlterLab Academic Skills suite.

alterlab-aeon

AlterLab-IEU/AlterLab-Academic-Skills

Runs time series machine learning with the aeon library — classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search via scikit-learn compatible APIs. Use when working with temporal data, sequential patterns, or time-indexed observations (univariate or multivariate) that need specialized algorithms beyond standard ML approaches. Part of the AlterLab Academic Skills suite.

alterlab-akademik-tesvik

AlterLab-IEU/AlterLab-Academic-Skills

Computes the annual Turkish academic-incentive (akademik teşvik) score for Devlet (state) university öğretim elemanı (academic staff) from a classified activity list, applying the verified Akademik Teşvik Ödeneği Yönetmeliği (2018/11834) Faaliyet Hesaplama Tablosu headline puanları (Proje 20, Araştırma 15, Yayın 30, Patent 30, Atıf 30, Tebliğ 20, Ödül 20) with the k (author-count), p (Q1 1/Q2 0.8/Q3 0.5/Q4 0.25), and r (project-role) coefficients via türü puanı = Σ(faaliyet oranları) × headline (MADDE 8/2), then enforcing the per-type headline ceilings, the 100 cap (MADDE 8/3), and the net-30 payment gate (MADDE 10/3) in a deterministic scripts/tesvik_score.py. Use when the user wants to calculate akademik teşvik puanı, check the en az 30 (net-30) threshold, apply TABLO 4 ceilings, or estimate teşvik eligibility; keeps its coefficients separate from doçentlik scoring. For doçentlik point eligibility prefer alterlab-docentlik-eligibility. Part of the AlterLab Academic Skills suite.

alterlab-alpha-vantage

AlterLab-IEU/AlterLab-Academic-Skills

Accesses real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API (requires a free API key from alphavantage.co). Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or calculating technical indicators (SMA, EMA, MACD, RSI, Bollinger Bands). Part of the AlterLab Academic Skills suite.

alterlab-alphafold

AlterLab-IEU/AlterLab-Academic-Skills

Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted structure with confidence metrics, ranking models, or checking self-consistency of a design. For co-folding a protein WITH a small-molecule ligand or predicting binding affinity prefer alterlab-boltz; for antibody–antigen or one-FASTA multi-entity complexes prefer alterlab-chai; to LOOK UP an already-computed structure prefer alterlab-alphafold-db; for ESM embeddings or inverse folding prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

alterlab-alphafold-db

AlterLab-IEU/AlterLab-Academic-Skills

Access the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, download PDB/mmCIF files, and analyze prediction confidence metrics (pLDDT, PAE). Use when a UniProt ID needs a computationally predicted 3D structure or when no experimental structure exists, for homology modeling, protein engineering, or structure-based drug discovery; for EXPERIMENTALLY determined structures (X-ray, cryo-EM, NMR) prefer alterlab-pdb, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

alterlab-anndata

AlterLab-IEU/AlterLab-Academic-Skills

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.

alterlab-aperta

AlterLab-IEU/AlterLab-Academic-Skills

Drives TÜBİTAK Açık Bilim Politikası (Open Science Policy) compliance and deposition into Aperta — TÜBİTAK ULAKBİM's national open archive at aperta.ulakbim.gov.tr — encoding the binding mandates (green-road deposit of the accepted manuscript on acceptance; open access within 6 months for fen/mühendislik (STEM) and 12 months for sosyal/beşeri (SSH); İlke-6 documentation when data must stay closed for KVKK/privacy reasons) and scaffolding a TÜBİTAK Veri Yönetim Planı / VYP (data management plan) at grant-application time. Use when depositing to Aperta, complying with the TÜBİTAK açık bilim policy, preparing a TÜBİTAK data management plan (VYP), reporting open-access compliance in a final report, or documenting a justified data embargo. For Zenodo/Dryad/OSF and international DMPs prefer alterlab-open-science; for the KVKK lawful-basis/anonymisation plan prefer alterlab-kvkk-dmp. Part of the AlterLab Academic Skills suite.

alterlab-arboreto

AlterLab-IEU/AlterLab-Academic-Skills

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regulatory interactions, build adjacency networks, or run the GRN-inference step of a SCENIC pipeline on large datasets. Part of the AlterLab Academic Skills suite.

alterlab-arxiv

AlterLab-IEU/AlterLab-Academic-Skills

Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject categories. Use when finding or fetching papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics, or resolving an arXiv ID to its metadata and PDF. Part of the AlterLab Academic Skills suite.

alterlab-astropy

AlterLab-IEU/AlterLab-Academic-Skills

Processes astronomy and astrophysics data with the Astropy Python library — celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, and world coordinate systems (WCS). Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or general astronomical data analysis. Part of the AlterLab Academic Skills suite.

alterlab-benchling

AlterLab-IEU/AlterLab-Academic-Skills

Integrates the Benchling R&D platform via its REST API and SDK — access the registry (DNA, proteins), inventory, ELN entries and workflows, build Benchling Apps, and query the Benchling Data Warehouse. Use when automating Benchling lab data management, syncing sample registry or inventory records, scripting ELN entries/workflows, or running SQL against the Benchling Data Warehouse. Part of the AlterLab Academic Skills suite.

alterlab-bgpt-search

AlterLab-IEU/AlterLab-Academic-Skills

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server, returning 25+ fields per paper (methods, results, sample sizes, quality scores, conclusions). Use when running a literature review or evidence synthesis, or when needing experimental details (sample sizes, effect sizes, methods, quality scores) that abstracts alone do not provide. Part of the AlterLab Academic Skills suite.

alterlab-bindingdb

AlterLab-IEU/AlterLab-Academic-Skills

Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the full TSV download, searching by target (UniProt ID), compound (SMILES), or pathogen. Use when looking up experimental binding constants, profiling inhibitors of a protein target, doing lead optimization, polypharmacology analysis, or structure-activity relationship (SAR) studies; for curated bioactivity mining or drug-like compound library screening at scale prefer alterlab-chembl instead. Part of the AlterLab Academic Skills suite.

alterlab-biopython

AlterLab-IEU/AlterLab-Academic-Skills

Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez — for quick one-off database lookups use gget, for unified multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.

alterlab-biorxiv

AlterLab-IEU/AlterLab-Academic-Skills

Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the AlterLab Academic Skills suite.

alterlab-bioservices

AlterLab-IEU/AlterLab-Academic-Skills

Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quick single-database lookups use gget, for sequence and file manipulation use biopython. Part of the AlterLab Academic Skills suite.

alterlab-blast

AlterLab-IEU/AlterLab-Academic-Skills

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. Part of the AlterLab Academic Skills suite.

alterlab-boltz

AlterLab-IEU/AlterLab-Academic-Skills

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protein-only or protein–protein folding without ligands prefer alterlab-alphafold; for antibody–antigen complexes prefer alterlab-chai; to dock a ligand into a FIXED receptor structure prefer alterlab-diffdock; to look up an existing structure prefer alterlab-pdb. Part of the AlterLab Academic Skills suite.

alterlab-borzoi

AlterLab-IEU/AlterLab-Academic-Skills

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional tracks from a DNA sequence, scoring a non-coding/regulatory variant's effect on expression or chromatin, or doing in-silico mutagenesis of a locus. To LOOK UP a variant's population frequency prefer alterlab-gnomad; for its clinical significance prefer alterlab-clinvar; for protein-structure effects prefer alterlab-alphafold; for single-cell foundation models prefer alterlab-scgpt. Part of the AlterLab Academic Skills suite.

alterlab-brenda

AlterLab-IEU/AlterLab-Academic-Skills

Access the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations, organism data, and substrate-specific enzyme information indexed by EC number. Use when looking up enzyme kinetics, turnover numbers, or substrate specificity for biochemical research and metabolic pathway analysis. Part of the AlterLab Academic Skills suite.

alterlab-causal-inference

AlterLab-IEU/AlterLab-Academic-Skills

Estimates causal effects from observational and quasi-experimental data — difference-in-differences, instrumental variables, regression discontinuity, panel fixed effects, propensity-score / doubly-robust methods, and heterogeneous treatment effects (CATE) — using the verified Python stack: statsmodels and linearmodels (PanelOLS, IV2SLS), pyfixest (feols, event studies, Sun-Abraham, did2s), DoWhy (identify -> estimate -> refute), EconML (LinearDML, CausalForestDML, DRLearner), and rdrobust for RD. It names the identifying assumption before estimating and runs a refutation/robustness check after. Use when the request mentions difference-in-differences, instrumental variables, regression discontinuity, fixed effects / panel causal estimation, propensity scores, or treatment-effect estimation from non-randomized data. For choosing the design first prefer alterlab-ssci-design-gate; for plain regression or descriptive stats prefer alterlab-statistical-analysis. Part of the AlterLab Academic Skills suite.

alterlab-cbioportal

AlterLab-IEU/AlterLab-Academic-Skills

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

alterlab-cellxgene

AlterLab-IEU/AlterLab-Academic-Skills

Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.

alterlab-chai

AlterLab-IEU/AlterLab-Academic-Skills

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.

alterlab-chembl

AlterLab-IEU/AlterLab-Academic-Skills

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

alterlab-cirq

AlterLab-IEU/AlterLab-Academic-Skills

Builds, simulates, and runs quantum circuits with Cirq, Google Quantum AI's framework for NISQ hardware, noise-aware low-level circuit design, and noise characterization. Use when targeting Google Quantum AI processors (Sycamore/Weber), designing noise-aware NISQ circuits, or running characterization experiments (randomized benchmarking, XEB). For IBM Quantum hardware and Qiskit Runtime prefer alterlab-qiskit; for gradient-trained quantum ML and hybrid quantum-classical models prefer alterlab-pennylane; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

alterlab-citation-graph

AlterLab-IEU/AlterLab-Academic-Skills

Free, key-less ResearchRabbit analog — builds a citation and co-citation graph around one or more seed papers using the OpenAlex API. Walks both directions of the citation network (works the seed cites and works that cite the seed), ranks the discovered neighbourhood by co-citation strength and bibliographic coupling to surface the papers most central to a topic's literature, and exports the network as GraphML (Gephi / Cytoscape / yEd) and JSON. Use when mapping a literature landscape, finding seminal or highly co-cited papers from a seed DOI, snowballing a reference network, building a citation map / co-citation analysis, or visualizing how a research area's papers connect — no API key required (polite mailto only). Part of the AlterLab Academic Skills suite.

alterlab-citation-mgmt

AlterLab-IEU/AlterLab-Academic-Skills

Manages citations for academic research — searches Google Scholar and PubMed for papers, extracts accurate metadata, validates citations, and generates properly formatted BibTeX entries. Use when finding papers, verifying citation information, converting DOIs to BibTeX, checking reference accuracy in scientific writing, or building a bibliography. Part of the AlterLab Academic Skills suite.

alterlab-citation-verifier

AlterLab-IEU/AlterLab-Academic-Skills

Verifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public scholarly APIs (Crossref, OpenAlex, Semantic Scholar, arXiv) with a polite mailto identifier, resolving DOI/arXiv IDs, fuzzy-matching title and authors (difflib SequenceMatcher ratio >=0.70), flagging retractions marked in Crossref (update-to) or OpenAlex (is_retracted), and emitting per-entry JSON verdicts mapped to the AlterLab citation-hallucination taxonomy (TF/PAC/IH/PH/SH). Accepts BibTeX, a DOI/arXiv ID list, or free-form references; degrades gracefully offline by emitting 'unverified' verdicts and never silently passing. Use when the request mentions verify citations, check references, fabricated or hallucinated references, fake DOI, retraction check, bibliography audit, or reference existence check. Does NOT write or draft papers — for authoring a manuscript (whose citation-check mode inserts citations) prefer alterlab-paper-writer instead. Part of the AlterLab Academic Skills suite.

alterlab-clinical-decision

AlterLab-IEU/AlterLab-Academic-Skills

Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms, supporting GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance, output as publication-ready LaTeX/PDF. Use when building a CDS document, cohort analysis, or treatment recommendation report for drug development, clinical research, or evidence synthesis, or when GRADE grading, hazard ratios, survival/waterfall plots, or biomarker stratification are requested. Part of the AlterLab Academic Skills suite.

alterlab-clinical-reports

AlterLab-IEU/AlterLab-Academic-Skills

Writes comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology, pathology, lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP notes, H&P, discharge summaries) — with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. Use when drafting a case report for journal publication, a radiology/pathology/lab diagnostic report, an ICH-E3 clinical study report (CSR) or SAE narrative, or SOAP/H&P/discharge patient records needing regulatory-compliant formatting. Part of the AlterLab Academic Skills suite.

alterlab-clinicaltrials

AlterLab-IEU/AlterLab-Academic-Skills

Query 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.

alterlab-clinpgx

AlterLab-IEU/AlterLab-Academic-Skills

Access 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/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

alterlab-clinvar

AlterLab-IEU/AlterLab-Academic-Skills

Query 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 by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.

alterlab-cobrapy

AlterLab-IEU/AlterLab-Academic-Skills

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite.

alterlab-cosmic

AlterLab-IEU/AlterLab-Academic-Skills

Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or interpreting mutational signatures for cancer research and precision oncology. Not for germline pathogenicity calls (use alterlab-clinvar) or interactive cohort visualization like OncoPrints and survival from study data (use alterlab-cbioportal). Part of the AlterLab Academic Skills suite.

alterlab-dask

AlterLab-IEU/AlterLab-Academic-Skills

Scales 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.