Browse Skills — Page 59

chatehr-clinician-assistant

swaruplab/operon

EHR Chat Assistant

chatfai-automation

ComposioHQ/awesome-claude-skills

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

chatgpt-app-submission

openai/plugins

Inspect a ChatGPT Apps MCP server codebase and generate chatgpt-app-submission.json with app info suggestions, tool hint justifications, test cases, and negative test cases, then report review-check findings and outputSchema warnings for submission review.

chatgpt-apps

openai/skills

Build, scaffold, refactor, and troubleshoot ChatGPT Apps SDK applications that combine an MCP server and widget UI. Use when Codex needs to design tools, register UI resources, wire the MCP Apps bridge or ChatGPT compatibility APIs, apply Apps SDK metadata or CSP or domain settings, or produce a docs-aligned project scaffold. Prefer a docs-first workflow by invoking the openai-docs skill or OpenAI developer docs MCP tools before generating code.

chatgpt-apps

seaworld008/Commonly-used-high-value-skills

Build, scaffold, refactor, and troubleshoot ChatGPT Apps SDK applications that combine an MCP server and widget UI. Use when Codex needs to design tools, register UI resources, wire the MCP Apps bridge or ChatGPT compatibility APIs, apply Apps SDK metadata or CSP or domain settings, or produce a docs-aligned project scaffold. Prefer a docs-first workflow by invoking the openai-docs skill or OpenAI developer docs MCP tools before generating code.

chatgpt-import

vellum-ai/vellum-assistant

Import conversation history from ChatGPT into Vellum

chats

superagi/skills

Interact with SuperAGI Sales platform via the Chat CLI

chatwoot

vm0-ai/vm0-skills

Chatwoot API for customer support. Use when user mentions "Chatwoot",

chatwork-automation

ComposioHQ/awesome-claude-skills

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

chea-api

aipoch/medical-research-skills

Access ChEA3 and Harmonizome ChEA data for transcription factor enrichment analysis and metadata retrieval. Use when the user needs to perform ChEA3 enrichment analysis on a gene set, get metadata about the ChEA dataset, or retrieve information about a specific transcription factor (attribute).

cheap-gas-nearby

NomaDamas/k-skill

Use when the user asks for nearby cheapest gas stations or 근처 가장 싼 주유소. Always ask the user's current location first, then use Kakao Map anchor resolution plus official Opinet fuel-price APIs.

chebi-skill

openai/plugins

Submit compact ChEBI 2.0 API requests for chemical search, compound lookup, ontology traversal, and structure metadata. Use when a user wants concise ChEBI summaries

check

indranilbanerjee/digital-marketing-pro

Run the unified pre-publish quality gate on marketing content — hallucination detection, claim verification, brand voice scoring, structure validation. Use before publishing any marketing copy.

check-accessibility

MicrosoftDocs/cloud-adoption-framework

Checks image accessibility compliance per Microsoft Learn standards. Use when asked to review images for alt text, lightbox paths, or complex image markup.

check-accessibility

AgnosticUI/agnosticui

Review component for accessibility issues

check-analogy-novelty

lyndonkl/claude

Cross-references each proposed analogy in a 5-framing set against substacker shared-context/analogy-catalog.md to flag reuse. Classifies each analogy as new, reused-from-catalog (and which entry), or adjacent-to-catalog (close to an existing entry but not identical). Prevents the writer from recycling "imagine a library" for the twentieth time. Use after generate-analogy-set and before presenting framings to the writer. Trigger keywords: novelty, catalog, analogy reuse, already used, imagine a library.

check-bin-obj-clash

microsoft/testfx

Detects MSBuild projects with conflicting OutputPath or IntermediateOutputPath. USE FOR: builds failing with 'Cannot create a file when that file already exists', 'The process cannot access the file because it is being used by another process', intermittent build failures that succeed on retry, or missing/overwritten outputs in multi-project or multi-targeting builds where bin/obj (or project.assets.json) collide. Common causes: shared OutputPath, missing AppendTargetFrameworkToOutputPath, extra global properties (e.g. PublishReadyToRun), or SetTargetFramework on a ProjectReference to a single-targeting project. DO NOT USE FOR: file access errors unrelated to MSBuild (OS-level locking), single-project single-TFM builds, non-MSBuild build systems.

check-corpus-readiness

lyndonkl/claude

Checks whether the substacker corpus has enough material to justify a Curator run. Counts published posts, time-gates against the last review, and reports go/no-go with the specific gate that failed. Use before any Curator run, and on cold start to decide whether to propose sections yet. Trigger keywords: readiness, corpus ready, gate check, cadence gate, pre-flight.

check-crewai-api

crewAIInc/skills

Current crewai 1.15.x API versus the 0.x API that coding assistants remember: imports, Agent/Task/Crew parameters and defaults, kickoff variants, CrewOutput fields, LLM model strings and provider extras, structured output (output_pydantic, response_model, response_format), guardrails, unified Memory, knowledge embedders, the `crewai create crew` wizard vs --classic, reset-memories flags, and removed features. Use when writing, reviewing, or debugging any crewai code, before trusting remembered crewai syntax, or when a user pastes errors like `cannot import name 'BaseTool' from 'crewai_tools'`, `cannot import name 'persist'`, `ShortTermMemory`, `Anthropic native provider not available`, `LiteLLM fallback package is not installed`, `got an unexpected keyword argument 'response_format'`, `OPENAI_API_KEY is required`, `If return type is annotated, it must be Tuple[bool, Any]`, or `result.pydantic is None`.

check-duplicates

dandye/ai-runbooks

"Check for duplicate or similar cases. Use before deep analysis to avoid investigating the same incident twice. Takes a CASE_ID and returns list of similar cases."

check-impl-against-spec

warpdotdev/oz-for-oss

Compare a pull request's implementation against spec context in spec_context.md and feed any material mismatches into review.json. Use during PR review when approved or repository spec context is available.

check-link-wallet

stripe/link-cli

Reads the connected Link account, the cards and bank accounts saved in its wallet, its saved shipping addresses, and the status of existing spend requests. Use when the user asks which Link account is connected, what payment methods or addresses Link has saved, or whether a Link purchase has been approved yet.

check-links

ballred/obsidian-claude-pkm

Find broken wiki-links in the vault. Read-only analysis — scans for [[links]] and verifies target files exist. No writes, no dependencies.

check-open-prs

lifinance/contracts

Personal PR inbox for LI.FI engineers — covers both outgoing PRs (yours) and incoming review queue (others'). Produces a single dry-run dashboard with (a) your OWN open PRs cross-referenced with their #dev-sc-review / #dev-backend-expansion-review Slack threads, split into REMIND-team / YOUR-ACTION / OWN-DRAFTS / STALE, and (b) OTHER developers' PRs posted in those channels that need your attention — unreviewed (potential pick up) or you-reviewed-and-dev-addressed (potential re-review). Always dry-run first with explicit approval gates before any Slack post or code change. Optional parallel sub-agent investigation per PR. Use when the user says "check open PRs", "check my open PRs", "PR triage", "what PRs need me", "review queue", "where do my PRs stand", "/check-open-PRs", or asks for a personal PR dashboard.

check-releases

TheBushidoCollective/han

Check release health and compare error rates across deployments

check-relevance

MicrosoftDocs/cloud-adoption-framework

Assesses whether guidance is still relevant and framed for modern Azure approaches. Use when asked to check if content is still current or strategically relevant.

check-reporting

Aperivue/medsci-skills

Check manuscript compliance with medical research reporting guidelines. Supports 47 guidelines including STROBE, STROBE-MR, RECORD, REMARK (prognostic tumor-marker studies), TARGET (target trial emulation), GATHER (burden-of-disease / health-estimate modeling), CONSORT, CONSORT-AI, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, ARRIVE, PRISMA, PRISMA-DTA, PRISMA-P, PRISMA-ScR (scoping reviews), CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, MI-CLEAR-LLM, SQUIRE 2.0, CLEAR, MOOSE, GRRAS, SWiM, AMSTAR 2, CHEERS 2022, CROSS (survey studies), SRQR and COREQ (qualitative research), and risk of bias tools (QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Generates item-by-item assessment with PRESENT/MISSING/PARTIAL status.

check-screenshots-content

github/copilot-app-for-beginners

Verify GitHub Copilot app screenshots match the course content. Use when running /check-screenshots-content, or when asked to confirm that app- prefixed screenshots in chapter assets folders are consistent with the README labels, button names, menu items, dialog options, and step-by-step instructions that reference them.

check-tools

oaustegard/claude-skills

Validates development tool installations across Python, Node.js, Java, Go, Rust, C/C++, Git, and system utilities. Use when verifying environments or troubleshooting dependencies.

check-trajectories-workflow

UKGovernmentBEIS/inspect_evals

Use Inspect Scout to analyze agent trajectories from evaluation log files. Runs default and custom scanners to detect external failures, formatting issues, reward hacking, and ethical refusals. Use when user asks to check/analyze agent trajectories. Trigger when the user asks you to run the "Check Agent Trajectories" workflow.

checking-freshness

astronomer/agents

Quick data freshness check. Use when the user asks if data is up to date, when a table was last updated, if data is stale, or needs to verify data currency before using it.

checking-model-compliance

matlab/simulink-agentic-toolkit

Use this skill when the user asks to check Simulink model compliance against a standard (MISRA, MAB, JMAAB, ISO 26262, ISO 25119, DO-178C, DO-254, IEC 61508, IEC 62304, EN 50128, CERT C/CWE, AUTOSAR), wants to run Model Advisor checks, or needs a compliance report with fix suggestions. For JMAAB/MAB, supplement deterministic checks with agentic review of uncheckable guidelines.

checkly

TerminalSkills/skills

Expert guidance for Checkly, the synthetic monitoring platform that runs Playwright-based browser checks and API checks from locations worldwide. Helps developers implement monitoring-as-code (MaC) with the Checkly CLI, set up API and browser checks, configure alerting, and integrate monitoring into CI/CD pipelines.

checkout

remotion-dev/remotion

Checkout a requested branch or ref in the Remotion repo, rename the current task to the associated PR title when running in Codex, then install dependencies and build. Use when the user asks to checkout a ref and prepare the workspace.

checkout-credential-review

github/gh-aw

Review code that performs git or gh operations against repository checkouts in gh-aw, checking that the right credentials are available at the right time and that sparseness, shallowness and credential-free factors are properly considered.

checkov

TerminalSkills/skills

Expert guidance for Checkov, the static analysis tool for infrastructure-as-code that scans Terraform, CloudFormation, Kubernetes, Helm, Dockerfile, and ARM templates for security misconfigurations and compliance violations. Helps developers integrate Checkov into CI/CD pipelines and write custom policies.

checkpoint-and-recover

yogsoth-ai/de-anthropocentric-research-engine

Checkpoint state before risky operations, detect anomalies, and recover gracefully

checkpoint-promotion

wshobson/agents

Gate fine-tuned checkpoints with drift budgets, paired comparison, and forgetting checks before promotion. Use after a training run produces a checkpoint, when deciding whether a tuned model ships, or when a promoted model needs re-gating against updated goldens.

checkpoint-resume

yonatangross/orchestkit

Rate-limit-resilient pipeline with checkpoint/resume for long multi-phase sessions. Saves progress to .claude/pipeline-state.json after each phase. Use when starting a complex multi-phase task that risks hitting rate limits, when resuming an interrupted session, or when orchestrating work spanning commits, GitHub issues, and large file changes.

checkpoint-resume-long-job

Tibsfox/gsd-skill-creator

Persist progress for long-running jobs (batched LLM calls, large ingestions, multi-hour syncs) so that a context reset, crash, or interrupt doesn't lose work. Use whenever a job iterates over N items and completing item K matters independently. Provides a resumable.mjs library pattern plus the skill's invocation heuristics.

checkr

BankrBot/skills

|

checkstyle-configuration

TheBushidoCollective/han

Use when configuring Checkstyle for Java projects with XML config, custom checks, properties, and module setup.

checkstyle-custom

TheBushidoCollective/han

Use when developing custom Checkstyle checks, filters, and plugin integrations for project-specific Java code standards.

checkstyle-rules

TheBushidoCollective/han

Use when applying Checkstyle built-in checks for Java code including naming conventions, code metrics, and suppressions.

cheerio

TerminalSkills/skills

>-

chef-assistant

lyndonkl/claude

Guides cooking through culinary principles, food science, and flavor architecture rather than rote recipe steps. Covers technique teaching (knife skills, sauces, searing, braising), food science (Maillard reaction, emulsions, brining), flavor troubleshooting (salt/acid/fat/heat balance), menu planning, ingredient substitutions, plating, and cultural cuisine exploration. Use when users mention cooking, recipes, chef, cuisine, flavor, technique, plating, food science, seasoning, or culinary questions.

chematagent-drug-discovery

swaruplab/operon

Chemical Lab Agent

chembl-database

aipoch/medical-research-skills

Query the ChEMBL database for bioactive molecules, targets, bioactivities, and approved drugs; use this when you need to filter by physicochemical properties (e.g., MW, LogP), chemical structure (SMILES), or retrieve drug mechanism information.

chembl-database-bioactivity

jaechang-hits/SciAgent-Skills

Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug mechanism/indication data.

chembl-molecule-search

InternScience/scp

Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

chembl-search

swaruplab/operon

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

chembl-skill

openai/plugins

Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints. Use when a user wants concise ChEMBL summaries

chemcrow-drug-discovery

swaruplab/operon

An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design.

chemical_patent_analysis

InternScience/scp

Chemical Patent & Novelty Analysis - Analyze chemical novelty: PubChem substructure CAS search, ChEMBL similarity search, compound synonyms, and literature. Use this skill for patent chemistry tasks involving get substructure cas get similarity by smiles get compound synonyms by name search literature. Combines 4 tools from 3 SCP server(s).

chemical_property_profiling

InternScience/scp

Chemical Property Profiling - Profile chemical properties: basic info, hydrophobicity, H-bonds, charges, and molecular complexity. Use this skill for physical chemistry tasks involving calculate mol basic info calculate mol hydrophobicity calculate mol hbond calculate mol charge calculate mol complexity. Combines 5 tools from 1 SCP server(s).

chemical_safety_assessment

InternScience/scp

Chemical Safety Assessment - Assess chemical safety: PubChem compound info, FDA drug data, ADMET prediction, and structural alerts from ChEMBL. Use this skill for chemical safety tasks involving get general info by compound name get warnings and cautions by drug name pred molecule admet get compound structural alert. Combines 4 tools from 4 SCP server(s).

chemical_structure_comparison

InternScience/scp

Chemical Structure Comparison - Compare chemical structures: get SMILES, analyze structures, compute similarity, and check PubChem records. Use this skill for cheminformatics tasks involving NameToSMILES ChemicalStructureAnalyzer calculate smiles similarity get compound by name. Combines 4 tools from 4 SCP server(s).

chemical-bonding

Tibsfox/gsd-skill-creator

Ionic, covalent, and metallic bonding, Lewis structures, VSEPR theory, molecular geometry, polarity, and intermolecular forces. Covers octet rule and exceptions, formal charge, resonance, sigma/pi bonds, orbital hybridization, electronegativity-driven bond classification, VSEPR electron-domain and molecular geometries, dipole moments, and the four intermolecular force types (London dispersion, dipole-dipole, hydrogen bonding, ion-dipole). Use when predicting molecular shapes, bond properties, or physical behavior from molecular structure.

chemical-mass-percent-calculation

InternScience/scp

Calculate mass percentages and stoichiometric ratios for chemical reactions and compound compositions.

chemical-property-lookup

swaruplab/operon

Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools.

chemical-storage-sorter

aipoch/medical-research-skills

Sort laboratory chemicals into safe storage groups by hazard classification (acids, bases, oxidizers, flammables, toxics). Identifies incompatible pairs, generates storage plans with warnings, and supports OSHA/NFPA compliance for lab safety.

chemical-structure-analysis

InternScience/scp

Analyze chemical structures from compound names to retrieve SMILES, molecular formulas, molecular weight, and LogP values.

chemical-structure-converter

aipoch/medical-research-skills

Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds. Supports SMILES validation, batch processing, structure standardization, and cheminformatics database preparation for drug discovery workflows.

chemist-analyst

swaruplab/operon

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chemistry-agent

swaruplab/operon

Autonomous chemical synthesis & analysis

chemistry-rdkit

microsoft/agora-workbench

Molecular analysis and cheminformatics using RDKit — SMILES handling, descriptor calculation, fingerprints, substructure search, similarity, clustering, and drug-likeness screening via domain tools and the execute_chemistry_code tool.

cherry-assistant-guide

CherryHQ/cherry-studio

Cherry Studio 产品知识库、源码路径索引、故障排查和页面导航。当用户询问 Cherry Studio 的功能、配置、报错、使用方法时触发。也适用于用户提到 provider、模型、知识库、Agent、MCP、OpenClaw、PDF、快捷短语等关键词的场景。

cherry-pick

microsoft/DirectXShaderCompiler

Cherry-pick a commit onto another branch and open the PR. Use when the user asks to cherry-pick or backport a commit or PR to a release branch.

cherry-pr-test

CherryHQ/cherry-studio

Test Cherry Studio PRs by checking out the branch, launching the Electron app in debug mode, and running interactive UI tests via CDP.

chezmoi-sync

terrylica/cc-skills

Interactive chezmoi drift check and sync. TRIGGERS - chezmoi sync, sync dotfiles, dotfile drift, chezmoi guard, chezmoi check.

chezmoi-workflows

terrylica/cc-skills

Dotfile backup and sync with chezmoi. TRIGGERS - chezmoi, dotfiles, sync dotfiles, backup configs, cross-machine sync.

chi

TerminalSkills/skills

>-

chibi-style

arjun988/blender-skills

Chibi and SD proportion art direction for Blender characters with oversized heads, simplified anatomy, and cute silhouette rules.

chief-ai-officer-advisor

alirezarezvani/claude-skills

Chief AI Officer advisory for startups: model build-vs-buy decisions (API vs fine-tune vs in-house), AI risk classification under EU AI Act + US state patchwork, AI cost economics (API-to-self-hosted breakeven), and AI team org evolution. Use when deciding whether to call an API or fine-tune, classifying AI use cases for regulatory risk, calculating when self-hosting pays off, sequencing AI hires, or when user mentions CAIO, AI strategy, model selection, foundation model, fine-tuning, EU AI Act, NIST AI RMF, AI governance, model risk, or AI economics. Strategic only — does not duplicate engineering AI/ML skills.

chief-customer-officer-advisor

alirezarezvani/claude-skills

Chief Customer Officer advisory for startups: retention decomposition (gross retention vs NRR honesty, churn root-cause taxonomy), customer segmentation strategy (differential investment across tiers + ICP fit scoring), CS team coverage model (pooled vs named CSM thresholds + ratio math), and CS team org evolution (CS vs Support vs AM distinctions). Use when designing retention strategy, segmenting customers for differential investment, sizing CS team, or sequencing CS hires. Strategic only — does not duplicate engineering/business-growth tactical skills.

chief-data-officer-advisor

alirezarezvani/claude-skills

Chief Data Officer advisory for startups: AI training data rights and consent provenance, data product strategy (warehouse vs lakehouse vs mesh, build-vs-buy), B2B customer-data-as-asset valuation and M&A readiness, data team org evolution. Use when deciding whether to train models on customer data, choosing data architecture, valuing data for fundraising or M&A, sequencing data hires, or when user mentions CDO, chief data officer, data strategy, data mesh, lakehouse, training data, data product, data monetization, or customer data asset. NOT a tactical data engineering skill — strategic decisions only.

chief-exec

Agile-V/agile_v_skills

Chief Executive Officer (CEO) orchestrator for strategic alignment, cross-C-suite coordination, board relations, crisis management, and executive decision governance. Orchestrates all C-suite agents and venture-strategist.

chief-finance

Agile-V/agile_v_skills

Chief Financial Officer (CFO) orchestrator for financial modeling, fundraising strategy, cash management, financial controls, board reporting, and unit economics governance. Orchestrates business-operations (finance) and venture-strategist (investor relations).

chief-of-staff

alirezarezvani/claude-skills

C-suite orchestration layer. Routes founder questions to the right advisor role(s), triggers multi-role board meetings for complex decisions, synthesizes outputs, and tracks decisions. Every C-suite interaction starts here. Loads company context automatically. Use when a founder question needs routing to the right advisor — e.g. 'should we raise now or cut burn?' — or when a multi-domain decision needs a board meeting convened.

chief-ops

Agile-V/agile_v_skills

Chief Operating Officer (COO) orchestrator for cross-functional execution, process design, delivery cadence governance, vendor escalation, resource arbitration, and operational playbooks. Orchestrates business-operations (ops), release-manager, agile-v-product-owner, gtm-executor.

chief-people

Agile-V/agile_v_skills

Chief People Officer (CHRO) orchestrator for organizational design, hiring, compensation, culture, performance management, DE&I, and talent development. Use when defining org structure, hiring plans, compensation bands, culture principles, or people operations.

chief-tech

Agile-V/agile_v_skills

Chief Technology Officer (CTO) orchestrator for architecture governance, build-vs-buy decisions, tech debt management, engineering standards, platform strategy, and security posture. Orchestrates rd-innovator, build-agent, observability-planner, threat-modeler.

chinese-code-review

jnMetaCode/superpowers-zh

中文 review 沟通参考——话术模板、分级标注（必须修复/建议修改/仅供参考）、国内团队常见反模式应对。仅在用户显式 /chinese-code-review 时调用，不要根据上下文自动触发。

chinese-commit-conventions

jnMetaCode/superpowers-zh

中文 commit 与 changelog 配置参考——Conventional Commits 中文适配、commitlint/husky/commitizen 中文模板、conventional-changelog 中文配置。仅在用户显式 /chinese-commit-conventions 时调用，不要根据上下文自动触发。

chinese-copyright-application

okooo5km/Skills4U

中国软件著作权申请材料生成工具。申请表直接输出 Markdown 提交，源程序/用户手册/设计说明书三份生成 LaTeX 并编译为 PDF。自动分析项目代码，生成四份材料（前后各30页共60页源程序、含页眉页脚的用户手册和设计说明书、Markdown 申请表），并做版本号一致性、模块覆盖双向核验、字数限制等信息一致性校验。适用于微信小程序、Web应用、移动App、桌面应用等各类软件项目。当用户提到软件著作权、软著申请、版权登记时必须使用此 Skill。当用户要为任何软件项目准备著作权材料、生成软著文档时也应使用。

chinese-documentation

jnMetaCode/superpowers-zh

中文文档排版参考——中英文空格、全半角标点、术语保留、链接格式、中文文案排版指北约定。仅在用户显式 /chinese-documentation 时调用，不要根据上下文自动触发。

chinese-git-workflow

jnMetaCode/superpowers-zh

国内 Git 平台配置参考——Gitee、Coding.net、极狐 GitLab、CNB 的 SSH/HTTPS/凭据/CI 接入差异与镜像同步配置。仅在用户显式 /chinese-git-workflow 时调用，不要根据上下文自动触发。

chinese-novelist

openakita/openakita

Guide AI to write Chinese novels and fiction with structured character creation, plot architecture (起承转合), dialog writing, scene description, and genre-specific techniques for 玄幻, 都市, 悬疑, and 言情 genres.

chinese-writing

openakita/openakita

Enforce modern Chinese writing standards including tone, spacing rules (Pangu), full-width punctuation, paragraph structure, and active voice. Provides specific guidelines for blog posts, error messages, UI text, and technical documentation.

chipseq-allele-specific-binding

swaruplab/operon

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

chipseq-chip-deep-learning

swaruplab/operon

Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

chipseq-chromatin-state-segmentation

swaruplab/operon

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

chipseq-cut-and-run-tag

swaruplab/operon

Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

chipseq-differential-binding

swaruplab/operon

Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

chipseq-motif-analysis

swaruplab/operon

Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in peaks, testing for known TF enrichment, scanning for motif instances, comparing motif content between conditions, or interpreting motifs from deep learning models.

chipseq-peak-annotation

swaruplab/operon

Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

chipseq-peak-calling

swaruplab/operon

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

chipseq-qc

swaruplab/operon

Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

chipseq-spike-in-normalization

swaruplab/operon

Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, and applies the Patel et al 2024 *Nat Biotechnol* review's failure-mode framework to validate that normalization is correctly applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

chipseq-super-enhancers

swaruplab/operon

Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Handles peak stitching parameters, ranking choices, hockey-stick inflection, marker choice (H3K27ac vs MED1/BRD4), and cross-condition comparison with spike-in normalization. Constructs core regulatory circuitry (Saint-Andre 2016) from SE-encoded TFs. Use when identifying cell-identity / cancer-associated regulatory domains, comparing super-enhancers between conditions, identifying master transcription factor networks, or predicting BET-inhibitor responsiveness.