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Semi-automated research assistant for academic research and software development, especially for computer science and AI researchers. Supports Claude Code, Codex CLI, and OpenCode across literature review, coding, experiments, reporting, writing, and project knowledge management. Branch note: the main branch is the Claude Code workflow. If you use Codex CLI, please see the codex branch. If you use OpenCode, please see the opencode branch. - 2026-03-31: Zotero smart-import workflow docs aligned — updated Claude Scholar's research-facing docs around the latest zotero-mcp public surface:zotero_add_items_by_identifier is now the default paper-import path,zotero_reconcile_collection_duplicates is the standard post-import cleanup step, source-aware PDF cascade behavior is documented more accurately, and public vs internal diagnostics are now clearly separated. - 2026-03-31: README onboarding refreshed — clarified that Claude Scholar is especially well-suited to computer science and AI researchers, added practical getting-started scenarios after installation, improved prerequisite and branch guidance, and made the “existing local md files must be manually merged” expectation much more explicit. - 2026-03-31: Installer and hook behavior tightened — the installer now preserves existing local CLAUDE.md /CLAUDE.zh-CN.md files while installing repo-managed sidecar copies, and the default hook summaries were trimmed to reduce noisy temp-file / uncommitted-file output while keeping safer write-guard behavior. - 2026-03-31: Japanese documentation added — added Japanese docs for the main README plus CLAUDE ,MCP_SETUP , andOBSIDIAN_SETUP , so the repository now has a more complete multilingual documentation surface. View older changelog - 2026-02-25: Codex CLI support — added codex branch supporting OpenAI Codex CLI with config.toml, 40 skills, 14 agents, and sandbox security - 2026-02-23: Added setup.sh installer — backup-aware incremental updates for existing~/.claude , auto-backupsettings.json , additive hooks/mcpServers/plugins merge - 2026-02-21: OpenCode support — Claude Scholar now supports OpenCode as an alternative CLI; switch to the opencode branch for OpenCode-compatible configuration - 2026-02-20: Bilingual config — translated CLAUDE.md to English for international readability; addedCLAUDE.zh-CN.md as Chinese backup; Chinese users can switch withcp CLAUDE.zh-CN.md CLAUDE.md - 2026-02-15: Zotero MCP integration — added /zotero-review and/zotero-notes commands, updatedresearch-ideation skill with Zotero integration guide, enhancedliterature-reviewer agent with Zotero MCP support for automated paper import, collection management, full-text reading, and citation export - 2026-02-14: Hooks optimization — restructured security-guard to two-tier system (Block + Confirm),skill-forced-eval now groups skills into 6 categories with silent scan mode,session-start limits display to top 5,session-summary adds 30-day log auto-cleanup,stop-summary shows separate added/modified/deleted counts; removed deprecated shell scripts (lib/common.sh, lib/platform.sh) - 2026-02-11: Major update — added 10 new skills (research-ideation, results-analysis, citation-verification, review-response, paper-self-review, post-acceptance, daily-coding, frontend-design, ui-ux-pro-max, web-design-reviewer), 7 new agents, 8 research workflow commands, 2 new rules (security, experiment-reproducibility); restructured CLAUDE.md; 89 files changed - 2026-01-26: Rewrote all Hooks to cross-platform Node.js; completely rewrote README; expanded ML paper writing knowledge base; merged PR #1 (cross-platform support) - 2026-01-25: Project open-sourced, v1.0.0 released with 25 skills (architecture-design, bug-detective, git-workflow, kaggle-learner, scientific-writing, etc.), 2 agents (paper-miner, kaggle-miner), 30+ commands (including SuperClaude suite), 5 Shell Hooks, and 2 rules (coding-style, agents) | Section | What it helps with | |---|---| | Why Claude Scholar | Understand the project positioning and target use cases. | | Core Workflow | See the end-to-end research pipeline from ideation to publication. | | Quick Start | Install Claude Scholar in full, minimal, or selective mode. | | Getting Started Scenarios | See a few realistic first-use scenarios after installation. | | Integrations | Learn how Zotero and Obsidian fit into the workflow. | | Primary Workflows | Browse the main research and development workflows. | | Supporting Workflows | See the background systems that strengthen the main workflow. | | Documentation | Jump to setup docs, configuration, and templates. | | Citation | Cite Claude Scholar in papers, reports, or project docs. | Claude Scholar is not an end-to-end autonomous research system that tries to replace the researcher. Its core idea is simple: human decision-making stays at the center; the assistant accelerates the workflow around it. That means Claude Scholar is designed to help with the heavy, repetitive, and structure-sensitive parts of research — literature organization, note-taking, experiment analysis, reporting, and writing support — while still keeping the key judgments in human hands: - which problem is worth pursuing, - which papers actually matter, - which hypotheses are worth testing, - which results are convincing, - and what should be written, submitted, or abandoned. In other words, Claude Scholar is a semi-automated research assistant, not a “fully automated scientist.” Claude Scholar is especially well-suited to: - computer science researchers who move between literature review, coding, experiments, and paper writing, - AI / ML researchers who need one assistant workflow spanning ideation, implementation, analysis, reporting, and rebuttal, - research engineers and graduate students who want stronger workflow structure without giving up human judgment, - and software-heavy academic projects that benefit from Zotero, Obsidian, CLI automation, and reproducible project memory. It can still help in other research settings, but its current workflow design is most aligned with computer science, AI, and adjacent computational research. - Ideation: turn a vague topic into concrete questions, research gaps, and an initial plan. - Literature: search, import, organize, and read papers through Zotero collections. - Paper notes: convert papers into structured reading notes and reusable claims. - Knowledge base: route durable knowledge into Obsidian across Papers / Knowledge / Experiments / Results / Writing , with round-level experiment reports stored underResults/Reports/ . - Experiments: track hypotheses, experiment lines, run history, findings, and next actions. - Analysis: generate strict statistics, real scientific figures, and analysis artifacts with results-analysis . - Reporting: produce a complete post-experiment report with results-report , then write it back into Obsidian. - Writing and publication: carry stable findings into literature reviews, papers, rebuttals, slides, posters, and promotion. - Claude Code - Git - (Optional) Python + uv for Python development - (Optional) Zotero + Galaxy-Dawn/zotero-mcp for literature workflows - (Optional) Obsidian for project knowledge-base workflows git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar bash /tmp/claude-scholar/scripts/setup.sh Windows: please use Git Bash or WSL to run the installer. The installer is backup-aware and incremental-update friendly: - updates repo-managed skills/commands/agents/rules/hooks/scripts/CLAUDE*.md , - backs up overwritten files to ~/.claude/.claude-scholar-backups// , - backs up settings.json tosettings.json.bak , - preserves an existing ~/.claude/CLAUDE.md and installs the repo-managed version as~/.claude/CLAUDE.scholar.md , - preserves an existing ~/.claude/CLAUDE.zh-CN.md and installs the repo-managed version as~/.claude/CLAUDE.zh-CN.scholar.md , - preserves your existing env , model/provider settings, API keys, permissions, and currentmcpServers values, - adds missing hook entries instead of replacing your entire hook set. Important CLAUDE note: if you already maintain your own ~/.claude/CLAUDE.md or ~/.claude/CLAUDE.zh-CN.md , review ~/.claude/CLAUDE.scholar.md and ~/.claude/CLAUDE.zh-CN.scholar.md after installation and manually merge the Claude Scholar sections you want into your own files. Do not assume the sidecar files are applied automatically. To update later: cd /tmp/claude-scholar git pull --ff-only bash scripts/setup.sh Install only a small research-focused subset: git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar mkdir -p ~/.claude/hooks ~/.claude/skills cp /tmp/claude-scholar/hooks/*.js ~/.claude/hooks/ cp -r /tmp/claude-scholar/skills/ml-paper-writing ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/research-ideation ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/results-analysis ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/results-report ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/review-response ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/writing-anti-ai ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/git-workflow ~/.claude/skills/ cp -r /tmp/claude-scholar/skills/bug-detective ~/.claude/skills/ Post-install: minimal/manual install does not auto-merge settings.json ; copy only the hooks or MCP entries you want from settings.json.template . If you already have your own ~/.claude/CLAUDE.md or ~/.claude/CLAUDE.zh-CN.md , also merge the relevant sections from this repo's Claude files into yours instead of blindly overwriting them. Copy only the parts you need: git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar cd /tmp/claude-scholar cp hooks/*.js ~/.claude/hooks/ cp -r skills/latex-conference-template-organizer ~/.claude/skills/ cp -r skills/architecture-design ~/.claude/skills/ cp agents/paper-miner.md ~/.claude/agents/ cp rules/coding-style.md ~/.claude/rules/ cp rules/agents.md ~/.claude/rules/ Post-install: selective/manual install does not auto-merge settings.json ; copy only the hooks or MCP entries you actually want from settings.json.template . If you already have your own ~/.claude/CLAUDE.md or ~/.claude/CLAUDE.zh-CN.md , merge the relevant sections from this repo's Claude files into yours instead of blindly overwriting them. Step 1: Install the Plugin /plugin marketplace add Galaxy-Dawn/claude-scholar /plugin install claude-scholar@claude-scholar This auto-loads all skills, commands, agents, and hooks. During installation, you can choose the scope: user (all projects) or project (single project). Step 2: Install Rules (Required) Claude Code plugins cannot distribute rules automatically. Install them manually: git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar # User-level (all projects) mkdir -p ~/.claude/rules cp /tmp/claude-scholar/rules/*.md ~/.claude/rules/ # Or project-level (current project only) mkdir -p .claude/rules cp /tmp/claude-scholar/rules/*.md .claude/rules/ Post-install: plugin installation does not auto-load CLAUDE.md or configure settings.json ; if you already have your own ~/.claude/CLAUDE.md or ~/.claude/CLAUDE.zh-CN.md , merge the relevant Claude Scholar sections into yours instead of assuming the plugin applies them automatically. If you need Zotero MCP or other integrations, see the Integrations section for manual setup. After installation, the simplest way to begin is to describe your task in natural language. You do not need to memorize the whole system first. Below are a few realistic starting points. You can say: Help me start research on [your topic]. I want a literature-grounded plan, the key open questions, and the next concrete steps. What Claude Scholar will typically help with: - clarify the topic and narrow the research question, - identify promising literature directions, - suggest an initial plan or hypothesis list, - optionally route the work into Zotero or Obsidian if you use them. You can say: Review my Zotero collection on brain foundation models and summarize the main directions, gaps, and promising next steps. Typical output: - paper grouping by theme, - a short literature synthesis, - gap analysis, - candidate research directions worth pursuing next. You can say: Analyze the results in this experiment folder, check what changed across runs, and write a decision-oriented summary. Typical output: - metric comparison, - ablation or error-analysis suggestions, - a result summary that highlights what is solid, what is weak, and what to run next. You can say: Help me draft the related work section for this project based on the current findings and paper notes. or: Help me write a rebuttal draft for these reviewer comments. Typical output: - a structured section draft, - improved argument flow, - clearer claims and evidence mapping, - follow-up points that still need support or verification. - Start with one concrete task, not a vague request for "everything." - If you already maintain your own local CLAUDE.md files, merge the Claude Scholar sections you want into them instead of assuming sidecar files apply automatically. - Zotero and Obsidian are optional, but they become much more useful when you want durable literature notes or project memory rather than one-off chat output. Claude Scholar is maintained for: - Claude Code — the primary installation target. - Codex CLI — supported workflow and documentation are available in this repo ecosystem. - OpenCode — supported as an alternative CLI workflow. The top-level workflow is the same: research, coding, experiments, reporting, and project knowledge management. Use Zotero when you want Claude Scholar to help with: - paper import via DOI / arXiv / URL, - collection-based reading workflows, - full-text access through Zotero MCP, - detailed paper notes and literature synthesis. See MCP_SETUP.md. Use Obsidian when you want Claude Scholar to maintain a filesystem-first research knowledge base: Papers/ Experiments/ Results/ Results/Reports/ Writing/ Daily/ See OBSIDIAN_SETUP.md. Complete academic research lifecycle — 7 stages from idea to publication. End-to-end research startup from idea generation to literature management. | Type | Name | One-line explanation | |---|---|---| | Skill | research-ideation | Turn vague topics into structured questions, gap analysis, and an initial research plan. | | Agent | literature-reviewer | Search, classify, and synthesize papers into an actionable literature picture. | | Command | /research-init | Start a new topic from literature search to Zotero organization and proposal drafting. | | Command | /zotero-review | Review an existing Zotero collection and generate a structured literature synthesis. | | Command | /zotero-notes | Batch-read a Zotero collection and create structured paper reading notes. | How it works - 5W1H Brainstorming: turn a vague topic into structured questions ( What / Why / Who / When / Where / How ). - Literature Search & Import: search pape