Claude Code Skills · page 127

Use when user asks about 藏传佛教, 噶举派, 大手印, phyag chen, 拙火, tummo, 那洛六法, 苦行, 闭关, 道歌, mgur, 米拉日巴, 玛尔巴, 上师瑜伽, 出离, 暇满, 中阴, 气脉明点, 觉受, nyams, 本觉, rig pa, or wants teaching in 米拉日巴尊者 Milarepa's voice. Triggers include "米拉日巴"、"密勒日巴"、"Milarepa"、"道歌"、"十万歌集"、"大手印"、"拙火"、"那洛六法"、"玛尔巴"、"噶举"、"白教"、"山洞修行"、"苦行"、"上师瑜伽"、"中阴"、"明空" — invoke whenever user's question touches Tibetan Kagyu / Mahāmudrā / yogi practice or asks about Milarepa's life and teachings, even without explicit request.

Use when user asks about 蕅益大师, 教宗天台, 行归净土, 六信, 弥陀要解, 教观纲宗, 灵峰宗论, 性相融会, 禅教律净, 念佛, 事持理持, 现前一念, 一念心性, 净土宗第九祖, 明末四大高僧, 占察忏, or wants teaching in 蕅益 Ouyi's voice. Triggers include "蕅益"、"智旭"、"弥陀要解"、"教宗天台"、"行归净土"、"六信"、"事持"、"理持"、"性相融会"、"禅教律净"、"教观纲宗"、"灵峰"、"现前一念"、"明末四大高僧"、"占察轮相" — invoke whenever user's question touches Ouyi's cross-school synthesis or Tiantai-Pureland integration, even without explicit request.

Use when user asks about 藏传, 格鲁派, Gelug, 黄教, 三主要道, 菩提道次第广论, lam rim, 密宗道次第广论, 应成中观, 缘起性空, 辨了不了义, 宗喀巴, Tsongkhapa, Je Rinpoche, 甘丹寺, 戒律, 因明, 月称, 入中论, or wants teaching in 宗喀巴大师 Tsongkhapa's voice. Triggers include "宗喀巴"、"杰仁波切"、"Je Rinpoche"、"格鲁"、"黄教"、"道次第"、"广论"、"三主要道"、"应成中观"、"辨了不了义"、"甘丹"、"达赖喇嘛传承根基" — invoke whenever user's question touches Gelug doctrine / lamrim / Madhyamaka prasaṅgika / Tibetan tantra-shastra studies, even without explicit request.

Use when user asks about 唯识, 法相宗, 阿赖耶识, 末那识, 三性, 遍计所执, 依他起, 圆成实, 五位百法, 因明, 转识成智, 种子, 熏习, 瑜伽师地论, 成唯识论, or wants teaching in 玄奘法师 Xuanzang's voice. Triggers include phrases like "唯识"、"法相"、"玄奘"、"阿赖耶"、"末那"、"三性"、"百法"、"因明"、"转识成智"、"种子"、"遍计所执"、"依他起"、"圆成实"、"五种不翻"、"唯识三十颂"、"瑜伽"、"慈恩" — invoke whenever user's question touches Yogācāra/Vijñānavāda doctrine, even without explicit request.

Use when user asks about 虚云, 参禅, 话头, 念佛是谁, 疑情, 开悟, 桶底脱落, 禅七, 行香, 丛林, 五宗兼嗣, 临济, 曹洞, 沩仰, 云门, 法眼, 老实修行, 头陀行, 持戒, 禅净双修, 云居山, 南华寺, or wants teaching in 虚云老和尚 Xuyun's voice. Triggers include "虚云"、"参话头"、"念佛是谁"、"疑情"、"禅七"、"行香"、"丛林规矩"、"桶底脱落"、"五宗"、"杯子扑落地"、"老实修行"、"头陀"、"禅堂"、"坐禅"、"数息" — invoke whenever user's question touches Chan practice, meditation methods, or monastic discipline, even without explicit request.

Use when user asks about 印光大师, 净土, 念佛, 持名念佛, 十念法, 摄耳谛听, 老实念佛, 信愿行, 带业往生, 仗佛慈力, 自力他力, 竖出横超, 往生, 极乐, 阿弥陀佛, 净土三经, 敦伦尽分, 闲邪存诚, 因果报应, 文钞, 一函遍复, or wants teaching in 印光大师 Yinguang's voice. Triggers include "印光"、"文钞"、"老实念佛"、"信愿行"、"带业往生"、"仗佛慈力"、"横超竖出"、"都摄六根"、"净念相继"、"敦伦尽分"、"闲邪存诚"、"因果"、"十念法"、"摄耳谛听"、"一函遍复"、"净土三经"、"往生" — invoke whenever user's question touches Pure Land practice, Amitabha recitation, or faith-vow-practice, even without explicit request.

Use when user asks about 天台宗, 止观, 一念三千, 三谛圆融, 五时八教, 摩诃止观, 法华经, or wants teaching in 智者大师 Zhiyi's voice. Triggers include phrases like "天台"、"智者大师"、"止观怎么修"、"三谛"、"法华"、"一心三观"、"判教"、"圆教"、"四种三昧" — invoke whenever user's question touches Tiantai doctrine, even without explicit request.

Create style-driven slide images strictly with the Image 2 model, assemble those images into image-only PPTX decks, and manage reusable visual style libraries from documents or visual references. Use when the user asks for a "PPT Skill", "风格驱动 PPT", "提炼风格做 PPT", "调用某个风格做 PPT", "图片版 PPT", "保存 PPT 风格", "列出 PPT 风格", "文档生成 PPT", "文章生成 PPT", "把文档做成演示文稿", or wants to extract, save, reuse, and apply visual style keywords specifically for visual slide/image deck creation.

Use when user asks about 中观, 空性, 缘起性空, 八不中道, 二谛, 世俗谛, 第一义谛, 戏论, 毕竟空, 不可得, 如幻, 离四句, 破自性, 难行道易行道, 龙树, or wants teaching in 龙树菩萨 Nāgārjuna's voice. Triggers include phrases like "空"、"中观"、"缘起"、"性空"、"八不"、"中道"、"二谛"、"世俗谛"、"第一义谛"、"戏论"、"毕竟空"、"不可得"、"如幻"、"离四句"、"涅槃与世间"、"龙树"、"中论"、"大智度论"、"十二门论"、"回诤论"、"易行道" — invoke whenever user's question touches Madhyamaka/emptiness/two-truths doctrine, even without explicit request.

Use ONLY when the user says they do not know which master or which teaching mode to use — 不知道问谁, 该找哪位祖师, 该用哪个模式, 有哪些法师, which master should I ask, help me choose. This is a router, not a teacher: it names a destination and stops. If the user asks an actual doctrinal or practice question, do NOT invoke this — let the matching master skill answer directly.

Analyzes Rails applications and generates comprehensive upgrade reports with breaking changes, deprecations, and step-by-step migration guides for Rails 2.3 through 8.1. Use when upgrading Rails applications, planning multi-hop upgrades, or querying version-specific changes. Based on FastRuby.io methodology and "The Complete Guide to Upgrade Rails" ebook.

Clean up after (or abandon) a Rails upgrade. Drop NextRails.next? and NextRails.current? branches and retire dual-boot scaffolding (Gemfile.next, Gemfile.next.lock, conditional Gemfile groups), keeping either the next or the current version. Trigger when the user says they are done with the upgrade, want to clean up dual-boot, want to drop NextRails branches, want to finish the upgrade, want to abandon or revert the upgrade attempt, want to roll back to the current Rails version, or want to pause this upgrade hop. Based on FastRuby.io's "Finishing an Upgrade" methodology, extended with an abandon/pause path.

Query and orchestrate Arkloop Activity Record local activity data. Covers browser history, search terms, screen time, bluetooth, shell commands, window focus, keyboard, mouse, clipboard, screen content (accessibility tree), microphone audio transcription, and Codex sessions.

Query the user's screen recordings, audio, UI elements, and usage analytics via the local Screenpipe REST API at localhost:3030. Use when the user asks about their screen activity, meetings, apps, productivity, media export, retranscription, or connected services.

Check Screenpipe health status, process state, and diagnose common issues

Retrieve and analyze Screenpipe CLI backend logs and desktop app logs for debugging

Drive real macOS applications through the CUA Driver MCP server when the user asks to inspect, operate, or automate visible desktop UI.

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한국 정부·공공기관 지원사업(창업지원, 사업화 자금, 입주공간, R&D, 바우처, 경진대회) 전수조사 및 프로젝트 적합성 판정 스킬. K-Startup·기업마당(bizinfo)·NIPA·KOCCA·SMTECH 공고를 크롤링해 현재 작업 폴더의 프로젝트(아이템) 프로필에 맞는 사업을 "즉시 지원 가능 / 요건 충족 시 / 변형하면 가능" 3단계로 분류하고 마감일·자격요건을 원문 검증해 보고서를 만든다. 사용자가 "지원사업 찾아줘", "정부지원", "창업지원 사업", "입주공간/사업화 자금 알아봐", "공모전/경진대회 조사", "우리 아이템에 맞는 지원사업", "K-Startup/기업마당 조사" 등을 요청하면 반드시 이 스킬을 사용한다. 이전에 조사한 적이 있는 프로젝트에서 "재조사", "새로 나온 지원사업 있나", "지난번 이후 뭐 올라왔나"를 물으면 diff 모드(증분 재조사)로 이 스킬을 사용한다. 특정 사이트를 지목하지 않아도 지원사업·보조금·정부과제 탐색 의도가 보이면 트리거된다. 단, 이미 운영 중인 소상공인·가게·점포·자영업자의 지원(소상공인 지원금, 정책자금 대출, 가게 시설개선, 소상공인24, 폐업·재기 지원)은 이 스킬이 아니라 sole-search 스킬을 사용한다. 신호가 섞이면(예: ''온라인 셀러 지원금'') 어느 쪽인지 한 번 묻는다. 사용자 신분보다 요청 목적이 우선이다 — 가게 사장이라도 신규 아이템 창업지원·R&D를 찾으면 ir-search. 한국 지원사업 전용.

Project memory workflow for init/upgrade, profile-aware setup, end session, normal/full close, file organization, document archiving, language switching, versioned update logs, rule review, status, wiki sync, and context recovery. Use for /project-butler, setup/初始化, foundation setup, profile setup, end session/收工, normal close, full close, foundation repair, organize files/整理文件, change language/切换语言, continue/接着上次, continue full context/全面回顾, review claude, sync wiki, status. Maintains project memory files. Runs version freshness check before trigger routing.

数学建模竞赛论文写作全流程指导。覆盖国赛(CUMCM)和美赛(MCM/ICM)，从论文结构规划、各章节撰写、模型检验、参考文献规范到最终格式检查。与math-modeling-solver形成"解题→写作"配对——可接收solver输出的论文草稿片段直接展开写作。当用户提及数学建模论文写作、建模比赛、国赛/美赛/电工杯/亚太杯/深圳杯/华为杯论文、CUMCM、MCM/ICM、数模论文结构、摘要写作、模型检验、灵敏度分析、latex建模模板、word建模排版、Memo/Letter写作、模型命名、Our Work流程图，或需要写/修改/优化/检查建模论文的任何部分时，都必须使用此 skill。

数学建模竞赛解题全流程指导。覆盖国赛(CUMCM)和美赛(MCM/ICM)全部题型(A-F)，提供12种问题本质分析、95+场景模型决策矩阵、5本算法Cookbook、11本完整例题Playbook、22个Python+7个MATLAB可运行代码模板。与math-modeling-paper形成"解题→写作"配对。当用户提及建模思路、选什么模型、怎么建模、赛题求解、粘贴赛题文本、美赛/国赛题目分析、CVaR/NSGA-II/Monte Carlo/时间序列/ANOVA/灰色关联、网络流/图论/生态建模、模型命名/Memo/Letter/Our Work流程图时，使用此skill。

把旅行行程做成美观、离线可读、手机优先的单文件 HTML（交互地图+每日时间轴+出发前订票提醒）。两种用法——只给目的地和天数让它帮你规划，或丢一份现成计划让它直接出页面。触发：旅行计划可视化、做旅行攻略网页、行程 HTML、travel plan visualization。

Generate genuinely beautiful, on-brand UI instead of generic "AI slop" — use whenever the user asks to build, design, style, or improve a UI, landing page, dashboard, app screen, or component, whenever a PRD/spec needs a design pass before implementation, whenever the user pastes reference images/Pinterest/Dribbble links and wants the app to look like them, or whenever the user complains the AI-generated UI looks generic, boring, cookie-cutter, or "like every other AI app." Make sure to trigger this even if the user doesn't say "design" explicitly — phrases like "make this look good", "build the frontend for X", "this looks like every other SaaS site", or "match this vibe" all qualify. Also triggers on two verbs, "study"/"extract the look of" a reference screenshot or URL, and "audit"/"review"/"why does this look AI-generated" for critiquing existing UI.

Turn a concept, feature description, blog post, or pitch into a single beautiful, on-brand illustration by matching it to a real unDraw illustration in a local library and recoloring it to the brand accent — genuine illustrator quality, not an AI-drawn approximation. Use whenever the user asks to "make an illustration," "create a graphic," "visualize this concept," "explain this visually," wants something "unDraw-style" or "Storyset-style," needs a hero/feature/blog illustration, or says an idea needs a picture. Trigger even if they don't name a style — "make something to explain X" or "I need a graphic for this tweet" both qualify.

Battle-tested Playwright patterns for writing, debugging, and scaling reliable test suites. Use when you need guidance for E2E, API, component, visual, accessibility, or security testing, plus CI/CD, CLI automation, page objects, and migration from Cypress or Selenium. TypeScript and JavaScript.

Production-ready CI/CD configurations for Playwright — GitHub Actions, GitLab CI, CircleCI, Azure DevOps, Jenkins, Docker, parallel sharding, reporting, code coverage, and global setup/teardown.

Battle-tested Playwright patterns for writing and debugging reliable E2E, API, component, visual, accessibility, and security tests. Use when you need locator strategy, assertions, fixtures, network mocking, auth flows, trace debugging, or framework recipes for React, Next.js, Vue, and Angular. TypeScript and JavaScript.

Step-by-step migration guides for moving to Playwright from Cypress or Selenium/WebDriver — command mappings, architecture changes, and incremental adoption strategies.

Automates browser interactions for testing and validating your own web applications using playwright-cli. Use when you need terminal-first browser control for navigation, form filling, screenshots, tracing, bound browser sessions, debugging, or generating Playwright test code. Only use against applications you own or have explicit authorization to test.

Page Object Model patterns for Playwright — when to use POM, how to structure page objects, and when fixtures or helpers are a better fit.

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Opentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; control thermocycler, heater-shaker, magnetic, temperature modules. Use pylabrobot for multi-vendor.

Interactive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan. Two APIs: Plotly Express (DataFrame) and Graph Objects (fine control). For static publication figures use matplotlib; for statistical grammar use seaborn.

Statistical visualization on matplotlib + pandas. Distributions (histplot, kdeplot, violin, box), relational (scatter, line), categorical, regression, correlation heatmaps. Auto aggregation/CIs. Use plotly for interactive; matplotlib for low-level.

Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.

Bayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.

Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible. Use statsmodels for frequentist, pymc for Bayesian, lifelines for parametric.

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Python statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference, diagnostics, and hypothesis tests. Use scikit-learn for ML; statistical-analysis for test choice.

DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.

Parse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS export. Use FlowKit for gating/compensation.

Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless screenshots. Core visualization for Python bioimage workflows. Use ImageJ/FIJI for macro processing; napari for Python-native interactive visualization and DL segmentation review.

Computer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100× faster than pure Python via C++. Use scikit-image for scientific morphometry/regionprops; OpenCV for real-time, video, classical feature extraction.

Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.

Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem. Use OpenCV for real-time video; CellPose for DL cell segmentation; napari for visualization.

Python library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI, image series via pims. Use for quantitative SPT and diffusion coefficient extraction from fluorescence or brightfield video.

Low-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control of every element. PNG/PDF/SVG export. Use seaborn for quick stats, plotly for interactive.

Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control. 40+ chart types with hover, zoom, pan, animation. Exports HTML or static PNG/SVG/PDF via kaleido. Use for volcano plots with gene hover, dose-response dashboards, expression heatmaps, 3D molecular views. Use seaborn for stats; matplotlib for publication figures.

Guide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by data structure, color theory for accessibility/print, figure composition, journal formatting (Nature, Cell, ACS), and common pitfalls. Consult when visualizing data or preparing submission figures.

Statistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions (histplot, kdeplot), categorical (boxplot, violinplot), relational (scatterplot, lineplot), regression (regplot, lmplot), matrix (heatmap, clustermap), grids (pairplot, FacetGrid). Use for quick statistical summaries; matplotlib for fine control; plotly for interactive HTML.

Guide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *, **, ***, ****), matplotlib bracket+asterisk implementation, and use with seaborn box/violin/bar plots. Use when preparing publication-ready figures with significance markers.

Fast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.

Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.

CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.

Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed for variant calling, IGV, or ENCODE pipelines.

Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.

Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.

Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.

GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.

Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.

Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For PCR/restriction/cloning use biopython-molecular-biology; for SAM/BAM use pysam.

Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

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Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.

Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns ClinSig, submitter data, conditions, HGVS. For GWAS use gwas-database; for variant consequence prediction use Ensembl VEP.

Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.

Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key). For clinical pathogenicity use clinvar-database; for population frequencies use gnomad-database.

DepMap CRISPR gene effect (Chronos) analysis: sign convention for essentiality, per-gene NaN-safe Spearman correlation, data loading/alignment. For general NaN-safe correlation see nan-safe-correlation; for quality filtering see degenerate-input-filtering.

ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.

ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments by assay/biosample/target; download BED/bigWig; retrieve SCREEN cCREs by region or gene. Use to annotate variants with regulatory tracks, find open chromatin in a cell type, or fetch peak files for ChIP/ATAC analysis. For regulatory variant scoring use regulomedb-database; for GWAS associations use gwas-database.

Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.

NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.

NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.

Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.

gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants. For clinical pathogenicity use clinvar-database; for GWAS use gwas-database.

NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.

JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis. For ChIP-seq peak motif discovery use homer-motif-analysis; for regulatory variant scoring use regulomedb-database.

KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.

Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking. For GWAS use gwas-database; for clinical pathogenicity use clinvar-database.

Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge graphs; ensembl-database for mouse genome annotations.

Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.

Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none). Use for GWAS hit prioritization, regulatory variant annotation, cis-regulatory discovery. Use clinvar-database for pathogenicity; gwas-database for trait associations.

Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair. Use for TF co-occupancy, regulatory annotation, and TF binding atlases. Use jaspar-database for PWM motifs; encode-database for ENCODE tracks.

Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores. Use for UCSC annotations; Ensembl REST API for Ensembl gene IDs and VEP variant annotation.

ETE Toolkit (ETE3): Python phylogenetic tree analysis and visualization. Parse Newick/NHX/PhyloXML, traverse/annotate nodes, render figures with TreeStyle/NodeStyle, integrate NCBI taxonomy, run PhyloTree comparative genomics. Use for species trees, gene family evolution, annotated tree figures.

De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER. findMotifsGenome.pl finds over-represented patterns vs background; annotatePeaks.pl assigns context (TSS distance, gene, repeat). Use after MACS3 to identify enriched TFs, annotate peaks with nearest genes, and validate ChIP-seq via the target motif.

Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.

NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.

Python library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index interval datasets for ML, search embedding space with BEDSpace, and evaluate embedding quality. Use for chromatin accessibility clustering, regulatory element classification, and cross-sample region comparison.

Rust-backed Python library for fast genomic token arithmetic and BED processing. High-performance BED I/O, interval set ops (intersect, merge, complement, subtract), region tokenization against a universe, universe construction. Use for preprocessing large BED collections and ML token vocabularies.

Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks) vs input/IgG; outputs BED narrowPeak/broadPeak for motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq and ATAC-seq; broad for H3K27me3, H3K9me3, and other broad marks.

Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. Use when running BUSCO QC, comparing assemblies, or reporting completeness. See also: prokka-genome-annotation for annotation workflows feeding BUSCO.

All-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects paired-end overlaps, emits HTML+JSON QC in one pass. 3-10x faster than Trim Galore/Trimmomatic. First step before STAR, BWA-MEM2, or Salmon.

Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, Trim Galore, featureCounts, Kallisto, Salmon, Picard, GATK logs; merges per-sample stats with plots. For NGS pipeline-wide QC. Use FastQC directly for single-sample; MultiQC for multi-sample reporting.