Analyze Id Eval Ranking
open-thoughts/OpenThoughts-Agent
Given a list of models (HF name stubs) that have valid agentic ID eval scores in Supabase, build a ranking table: raw per-benchmark accuracy on the 3 ID benchmarks (SWE-Bench-100…
Multi-route literature expansion + metadata normalization for evidence-first surveys.
Install Literature Engineer
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills literature-engineer --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.codex/skills/literature-engineer .claude/skills/literature-engineer && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "literature-engineer" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineer into .claude/skills/literature-engineer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-engineer", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineerType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills literature-engineer --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.codex/skills/literature-engineer .agents/skills/literature-engineer && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "literature-engineer" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineer into .agents/skills/literature-engineer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-engineer", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills literature-engineer --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.codex/skills/literature-engineer .cursor/skills/literature-engineer && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "literature-engineer" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineer into .cursor/skills/literature-engineer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-engineer", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/WILLOSCAR/research-units-pipeline-skills.git --path .codex/skills/literature-engineer--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills literature-engineer --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.codex/skills/literature-engineer .gemini/skills/literature-engineer && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "literature-engineer" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineer into .gemini/skills/literature-engineer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-engineer", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install WILLOSCAR/research-units-pipeline-skills literature-engineerInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/.codex/skills/literature-engineer .github/skills/literature-engineer && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "literature-engineer" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineer into .github/skills/literature-engineer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-engineer", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install WILLOSCAR/research-units-pipeline-skills literature-engineer --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/WILLOSCAR/research-units-pipeline-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.codex/skills/literature-engineer .opencode/skills/literature-engineer && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "literature-engineer" agent skill from https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/literature-engineer into .opencode/skills/literature-engineer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "literature-engineer", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
literature-engineer- GitHub stars
- 513
- Token cost
- ~1.5k tokens
- SKILL.md length
- 638 words
- Files
- 5 (incl. scripts, references, assets)
- Skills in repo
- 107
- Repo updated
- First seen
- Licence
- None found
At a glance
Multi-route literature expansion + metadata normalization for evidence-first surveys.
- Works in 5 steps: Offline-first merge: ingest all… → Online retrieval (optional): if enabled,… → Snowballing (optional): expand from seed… → …
- Tasks that involve Database schema design
- SKILL.md covers Triggers & routing, Load Order, Script Boundary and Inputs, plus 5 more sections
- Runs Python scripts from its folder; calls uv
What it does
Literature Engineer is an agent skill from WILLOSCAR/research-units-pipeline-skills. Multi-route literature expansion + metadata normalization for evidence-first surveys.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 8 other files, including scripts, reference files and assets (for example `assets/domain_packs/embodied_ai.json`, `assets/domain_packs/llm_agents.json` and `references/domain_pack_overview.md`).
It sits in Research & Science, covering Database schema design. It works with arXiv. The repository describes itself as: Research pipelines as semantic execution units: each skill declares inputs/outputs, acceptance criteria, and guardrails. Evidence-first methodology prevents hollow writing…
When your agent uses it
- Tasks that involve Database schema design
Example prompts
- “/literature-engineer”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Offline-first merge: ingest all available offline exports (and label provenance per file).
- Online retrieval (optional): if enabled, run arXiv API retrieval for each keyword query.
- Snowballing (optional): expand from seed papers via references/cited-by (online), or merge offline snowball exports.
- Normalize + dedupe: canonicalize IDs/URLs, merge duplicates while unioning provenance.
- Report: write a concise retrieval report with coverage buckets and missing-meta counts.
What it can do on your machine
Read from SKILL.md and the folder at commit c92912a. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uv
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use uv, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Literature Engineer loads about 1.5k tokens when it runs, and up to ~1.8k if it reads all its reference files. Until then it costs about 26 tokens; SKILL.md has 638 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 638 words (~1,494 tokens).
“Goal: build a large, verifiable candidate pool for downstream dedupe/rank, mapping, notes, citations, and drafting.”
- name
- literature-engineer
Files
SKILL.md and 4 other files (scripts, references, assets) in .codex/skills/literature-engineer of WILLOSCAR/research-units-pipeline-skills.
- SKILL.md
- assets/domain_packs/embodied_ai.json
- assets/domain_packs/llm_agents.json
- references/domain_pack_overview.md
- scripts/run.py
Open the folder on GitHubat commit c92912a
Compare with similar skills
Literature Engineer next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Literature Engineer this skillWILLOSCAR/research-units-pipeline-skills | 513 | — | ~1.5k | Automated safety check: Pass | None | |
| Analyze Id Eval Rankingopen-thoughts/OpenThoughts-Agent | 301 | — | ~3.1k | Automated safety check: Pass | Apache-2.0 | |
| Bio Chipseq Differential BindingGPTomics/bioSkills | 1.2k | 2 repos | ~5.1k | Automated safety check: Pass | MIT | |
| Bio Geo DataGPTomics/bioSkills | 1.2k | 2 repos | ~4.4k | Automated safety check: Pass | MIT | |
| Tooluniverse Metabolomics Analysiswu-yc/LabClaw | 1.1k | 2 repos | ~5.9k | Automated safety check: Pass | None | |
| Bio Spatial Transcriptomics Spatial PreprocessingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None |
Similar skills
Bio Chipseq Differential Binding
GPTomics/bioSkills
Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2.
Bio Geo Data
GPTomics/bioSkills
Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror.
Tooluniverse Metabolomics Analysis
wu-yc/LabClaw
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux.
Bio Spatial Transcriptomics Spatial Preprocessing
FreedomIntelligence/OpenClaw-Medical-Skills
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data.
Gene Protein Expression Matrix Normalization
aipoch/medical-research-skills
A skill your agent uses when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory…
More from WILLOSCAR/research-units-pipeline-skills
All 107 skills in this repoAppendix Table Writer
WILLOSCAR/research-units-pipeline-skills
Curate reader-facing survey tables for the Appendix (clean layout + high information density), using only in-scope evidence and existing citation keys.
Artifact Contract Auditor
WILLOSCAR/research-units-pipeline-skills
Audit one research Workspace for declared Unit outputs and Pipeline target Artifacts, writing output/CONTRACTREPORT.md; use for mid-Run coverage snapshots or final delivery completeness, not deep…
Arxiv Search
WILLOSCAR/research-units-pipeline-skills
Retrieve arXiv paper metadata with keyword queries or import an offline arXiv export, and save results as JSONL (papers/papersraw.jsonl).
Chapter Lead Writer
WILLOSCAR/research-units-pipeline-skills
Write H2 chapter lead blocks (sections/S<secidlead.md) that preview the chapter's comparison lens and connect its H3 subsections, without adding new facts.
Chapter Skeleton
WILLOSCAR/research-units-pipeline-skills
Build a retrieval-informed chapter skeleton (outline/chapterskeleton.yml) from taxonomy/core scope before stable H3 decomposition.
Dedupe Rank
WILLOSCAR/research-units-pipeline-skills
A skill your agent uses when a broad paper candidate pool needs deterministic deduplication and a stable core set.
Related
Works with
Categories
Questions about Literature Engineer
What does Literature Engineer do?
Multi-route literature expansion + metadata normalization for evidence-first surveys. Literature Engineer is an agent skill from WILLOSCAR/research-units-pipeline-skills. Multi-route literature expansion + metadata normalization for evidence-first surveys.
When should I use Literature Engineer?
Literature Engineer fits situations like: tasks that involve Database schema design.
How do I install Literature Engineer in Claude Code?
Run `npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a claude-code`. Or copy the skill folder (.codex/skills/literature-engineer in WILLOSCAR/research-units-pipeline-skills) into .claude/skills/literature-engineer in your project. Claude Code loads it when a task matches its description.
How do I install Literature Engineer in Codex?
Run `npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a codex`. Or copy the skill folder (.codex/skills/literature-engineer in WILLOSCAR/research-units-pipeline-skills) into .agents/skills/literature-engineer in your project. Codex loads it when a task matches its description.
Can I use Literature Engineer in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add WILLOSCAR/research-units-pipeline-skills --skill literature-engineer -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/literature-engineer, .gemini/skills/literature-engineer, .github/skills/literature-engineer and .opencode/skills/literature-engineer in your project.
What does Literature Engineer need to run?
Going by SKILL.md and its folder, Literature Engineer needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Literature Engineer access the network?
SKILL.md contains no URLs. Its commands use uv, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Literature Engineer safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Literature Engineer use?
No licence was found for Literature Engineer or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Literature Engineer use?
About 1.5k tokens (SKILL.md is roughly 6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 258 tokens, read only when the agent opens those files.
What are the alternatives to Literature Engineer?
Skills that share tags, products or a category with Literature Engineer: Analyze Id Eval Ranking (open-thoughts/OpenThoughts-Agent, 301 stars), Bio Chipseq Differential Binding (GPTomics/bioSkills, 1.2k stars), Bio Geo Data (GPTomics/bioSkills, 1.2k stars) and Tooluniverse Metabolomics Analysis (wu-yc/LabClaw, 1.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Literature Engineer?
WILLOSCAR (a GitHub user) maintains it in WILLOSCAR/research-units-pipeline-skills, which has 513 GitHub stars. The repository holds 107 skills in this directory. The repository was last updated on October 5, 2026.
Source: WILLOSCAR/research-units-pipeline-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.