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Updated 2w ago

by flonat

flonat-research

Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows

Works with
  • Claude
  • Codex

146 GitHub stars (146)

+2 in 16 days

Stars gained per day · daily snapshots since Sep 30
Stars gained per day, Sep 30 to Oct 16: +2 in total; the busiest day was Oct 5 with +1 stars.Oct 1: 0 starsOct 2: 0 starsOct 3: 0 starsOct 4: 0 starsOct 5: +1 starsOct 6: 0 starsOct 7: 0 starsOct 8: 0 starsOct 9: +1 starsOct 10: 0 starsOct 11: 0 starsOct 12: 0 starsOct 13: 0 starsOct 14: 0 starsOct 15: 0 starsOct 16: 0 stars
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  • 30 skills (30 skills found in its SKILL.md files)
  • 28 forks (28 forks)
  • 2w ago last update (Last updated 2w ago)

Install

Skills CLI

npx skills add flonat/flonat-research

Asks which skills and agents to install. Just one: npx skills add flonat/flonat-research --skill beamer-deck — add -g for every project.

Claude Code

git clone https://github.com/flonat/flonat-researchcp -r "flonat-research/skills/beamer-deck" ~/.claude/skills/

Copies the beamer-deck skill into ~/.claude/skills/ for every project (use .claude/skills/ for one project). Repeat for the other skills listed below.

Plugin

/plugin marketplace add flonat/flonat-research

Run inside Claude Code if the repository ships a plugin marketplace, then pick plugins from /plugin.

Skills can run code on your machine — read the SKILL.md first.

What it does

In the author's own words, from each skill's SKILL.md — showing the first 30 of 87 files.

  • beamer-deck

    Create an academic presentation as a LaTeX Beamer source and reviewed PDF with an original theme. Use when the requested deliverable is a conference, seminar, or lecture deck in Beamer. Not for PowerPoint or RevealJS; use $pptx or $quarto-deck.

    skills/beamer-deck/SKILL.md on GitHub (opens in a new tab)
  • bib-coverage

    Compare a project .bib against a Paperpile project/topic folder to find uncited papers or unfiled entries. Use when the user asks to compare a project .bib against a Paperpile project/topic folder to find uncited papers or unfiled entries.

    skills/bib-coverage/SKILL.md on GitHub (opens in a new tab)
  • bib-filter

    Filter a LaTeX project's bibliography to the entries actually cited, with Overleaf-source resolution, temporary staging, validation, approval-gated canonical replacement, and compilation. Use before submission or after large revisions.

    skills/bib-filter/SKILL.md on GitHub (opens in a new tab)
  • bib-parse

    Extract citations from a PDF and generate a validated .bib file. Use when the user asks to extract citations from a PDF and generate a validated .bib file. Reads the PDF, identifies referenced works, constructs BibTeX entries, and verifies metadata.

    skills/bib-parse/SKILL.md on GitHub (opens in a new tab)
  • brief-compliance-check

    Check a LaTeX coursework submission against the requirements in a supplied PDF assessment brief. Use when verifying format, required sections, word limits, or deliverables before submission. Not for general prose proofreading; use $proofread.

    skills/brief-compliance-check/SKILL.md on GitHub (opens in a new tab)
  • camera-ready

    Convert an accepted anonymous-submission LaTeX paper (AAAI/AIES/ACM-style) to camera-ready and implement the accepted reviews. Use when a paper is accepted with no rebuttal and you need to de-anonymize, add copyright, turn on section numbering, implement each reviewer's minor revisions, optionally move proofs to a non-counted appendix, and QA. Not for R&R/revise-and-resubmit (use strategic-revisi…

    skills/camera-ready/SKILL.md on GitHub (opens in a new tab)
  • causal-design

    Design or audit the identification strategy for an observational study. Use when the task concerns estimands, causal assumptions, threats to identification, or defensible research design rather than model implementation.

    skills/causal-design/SKILL.md on GitHub (opens in a new tab)
  • checkpoint

    Save a compact continuation checkpoint so current work survives context compaction or a later session. Use when the active context is becoming long or work must pause without changing client or machine ownership. For an explicit cross-session/client transfer, use $handoff.

    skills/checkpoint/SKILL.md on GitHub (opens in a new tab)
  • code-archaeology

    Recover the structure, intent, and lineage of old code, data, or analysis files. Use when inherited or dormant research code must be understood before it is changed. Not for a quality review of already-understood code.

    skills/code-archaeology/SKILL.md on GitHub (opens in a new tab)
  • compile-knowledge

    Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki. Use when project evidence is scattered across source records and needs synthesis into durable articles. Not for promoting existing articles into the global vault wiki; use $wiki-grow.

    skills/compile-knowledge/SKILL.md on GitHub (opens in a new tab)
  • computational-experiments

    Scaffold, execute, analyse, and publish computational research experiments through a reproducible staged workflow. Use when a research question requires simulations or computational sweeps rather than a one-off script.

    skills/computational-experiments/SKILL.md on GitHub (opens in a new tab)
  • cross-language-check

    Replicate a quantitative analysis in a second language (R↔Python↔Stata↔Julia) and compare outputs for implementation errors. Use when an existing empirical result needs independent cross-language verification. Not for reviewing one implementation in place; use $code-suite.

    skills/cross-language-check/SKILL.md on GitHub (opens in a new tab)
  • data-analysis

    Deliver an end-to-end analysis pipeline: EDA, estimation, or publication output. Use when the user requests an end-to-end analysis pipeline: EDA, estimation, or publication output.

    skills/data-analysis/SKILL.md on GitHub (opens in a new tab)
  • devils-advocate

    Adversarially challenge research assumptions, mechanisms, and arguments in writing. Use when stress-testing a claim or design before committing to it. Not for an interactive oral drill or a full referee report; use $grill-me or a review agent.

    skills/devils-advocate/SKILL.md on GitHub (opens in a new tab)
  • docs-consistency

    Review user-facing documentation for accuracy, consistency, and completeness across private, public, nested repos, and the user manual. Use when docs feel stale, after major changes, or before sharing. (Replaces `repo-doc-audit`)

    skills/docs-consistency/SKILL.md on GitHub (opens in a new tab)
  • docx

    Create, read, edit, or convert Microsoft Word documents while preserving professional document structure. Use when a .docx file is a primary input or requested output, including tracked changes, comments, images, headings, page furniture, or polished reports and letters. Not for PDFs, spreadsheets, Google Docs, or unrelated coding tasks.

    skills/docx/SKILL.md on GitHub (opens in a new tab)
  • experiment-design

    Design empirical studies through power analysis, pre-analysis planning, QSF parsing, and survey architecture. Use when specifying sampling, measurement, treatment, or analysis before data collection. Not for causal identification alone; use $causal-design.

    skills/experiment-design/SKILL.md on GitHub (opens in a new tab)
  • grill-me

    Run an interactive one-question-at-a-time oral drill for research defence or active-recall study, escalating around weak answers and ending with a study sheet. Use when the user asks to be grilled, quizzed, or prepared for a viva, job talk, seminar, or exam. Not for a written critique; use $devils-advocate or a review agent.

    skills/grill-me/SKILL.md on GitHub (opens in a new tab)
  • handoff

    Create, accept, or update the persistent `.context/ai-handoff.md` state shared by AI sessions and machines. Use when continuing in a new Claude or Codex session, transferring work between clients, or recording ownership and restart state.

    skills/handoff/SKILL.md on GitHub (opens in a new tab)
  • ideas

    Capture and integrate improvement ideas for the shared Claude Code and Codex infrastructure. Use when recording an infrastructure enhancement for later review rather than implementing it immediately.

    skills/ideas/SKILL.md on GitHub (opens in a new tab)
  • init-project-course

    Bootstrap a university course or module folder with the canonical teaching structure, guidance, and starter files. Use when creating or migrating a course workspace. Not for checking an existing course without modifying it; use $audit-project-course.

    skills/init-project-course/SKILL.md on GitHub (opens in a new tab)
  • init-project-light

    Bootstrap a lightweight project with minimal guidance, context, and repository structure. Use when a small non-research project needs durable AI collaboration without the full research or course scaffold. Not for formal research projects; use $init-project-research.

    skills/init-project-light/SKILL.md on GitHub (opens in a new tab)
  • init-project-orchestration

    Create or migrate project-level agents, repeatable project workflows, and planning state from one client-neutral contract, then render repository-scoped adapters for both Claude Code and Codex. Use when a research project needs role separation, project commands, formal phase tracking, or conversion from an existing Claude-only .claude/agents and .claude/commands setup.

    skills/init-project-orchestration/SKILL.md on GitHub (opens in a new tab)
  • init-project

    Bootstrap a new research project. Interview for details, scaffold directory structure, create Overleaf symlink, initialise git, and create project context files.

    skills/init-project/SKILL.md on GitHub (opens in a new tab)
  • insights-deck

    Archive an exported Claude Code insights HTML report and turn it into a timestamped Beamer presentation usable from either client. Use when the insights export is the source artifact for a presentation. Not for a general research talk; use $talk-deck.

    skills/insights-deck/SKILL.md on GitHub (opens in a new tab)
  • interview-me

    Conduct an adaptive structured interview that elicits tacit knowledge, requirements, preferences, or decisions and summarizes them explicitly. Use when the needed information is in the user's head and cannot be recovered from project files. Not for adversarial oral examination; use $grill-me.

    skills/interview-me/SKILL.md on GitHub (opens in a new tab)
  • knowledge-lint

    Lint an existing project knowledge base for contradictions, uncited claims, missing connections, stale articles, and orphaned concepts. Use when checking the integrity of already compiled knowledge before relying on or expanding it. Not for compiling raw sources; use $compile-knowledge.

    skills/knowledge-lint/SKILL.md on GitHub (opens in a new tab)
  • latex-diff

    Compare two LaTeX files, project directories, or Git revisions and produce human-readable plus machine-readable severity-graded semantic changes. Use when determining what changed between manuscript versions or preparing a revision audit bundle. Not for proofreading one version; use $proofread.

    skills/latex-diff/SKILL.md on GitHub (opens in a new tab)
  • latex-health-check

    Compile all LaTeX projects and report cross-project build consistency. Use when checking whether a collection of papers builds cleanly. Not for rendered visual inspection after a clean build; use $latex-polish.

    skills/latex-health-check/SKILL.md on GitHub (opens in a new tab)
  • latex-polish

    Inspect a cleanly compiling LaTeX document for source pathologies and rendered visual defects by linting and viewing selected PDF pages. Use when compilation succeeds but title pages, floats, tables, figures, or layout still need publication-quality review. Not for basic compilation health; use $latex-health-check.

    skills/latex-polish/SKILL.md on GitHub (opens in a new tab)

Review before you install

A skill is a set of instructions and scripts your agent will follow, and it can run code on your machine. Read the SKILL.md and any scripts first — this listing is not a security review.