Instrument Data To Allotrope
aws-samples/amazon-bedrock-agents-healthcare-lifesciences
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV.
Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook…
Install Spreadsheet Ops
$ npx skills add aipoch/medical-research-skills --skill spreadsheet-ops -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills spreadsheet-ops --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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/scientific-skills/Other/spreadsheet-ops .claude/skills/spreadsheet-ops && 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 "spreadsheet-ops" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-ops into .claude/skills/spreadsheet-ops/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-ops", 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/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-opsType 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 aipoch/medical-research-skills --skill spreadsheet-ops -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills spreadsheet-ops --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/scientific-skills/Other/spreadsheet-ops .agents/skills/spreadsheet-ops && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "spreadsheet-ops" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-ops into .agents/skills/spreadsheet-ops/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-ops", 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 aipoch/medical-research-skills --skill spreadsheet-ops -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills spreadsheet-ops --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/scientific-skills/Other/spreadsheet-ops .cursor/skills/spreadsheet-ops && 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 "spreadsheet-ops" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-ops into .cursor/skills/spreadsheet-ops/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-ops", 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/aipoch/medical-research-skills.git --path scientific-skills/Other/spreadsheet-ops--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 aipoch/medical-research-skills --skill spreadsheet-ops -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills spreadsheet-ops --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/scientific-skills/Other/spreadsheet-ops .gemini/skills/spreadsheet-ops && 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 "spreadsheet-ops" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-ops into .gemini/skills/spreadsheet-ops/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-ops", 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 aipoch/medical-research-skills spreadsheet-opsInstalls 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 aipoch/medical-research-skills --skill spreadsheet-ops -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/scientific-skills/Other/spreadsheet-ops .github/skills/spreadsheet-ops && 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 "spreadsheet-ops" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-ops into .github/skills/spreadsheet-ops/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-ops", 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 aipoch/medical-research-skills --skill spreadsheet-ops -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills spreadsheet-ops --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/scientific-skills/Other/spreadsheet-ops .opencode/skills/spreadsheet-ops && 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 "spreadsheet-ops" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/spreadsheet-ops into .opencode/skills/spreadsheet-ops/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "spreadsheet-ops", 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
spreadsheet-ops- GitHub stars
- 2k
- Token cost
- ~1.7k tokens
- SKILL.md length
- 757 words
- Files
- 18 (incl. scripts, references)
- Skills in repo
- 567
- Repo updated
- First seen
- Licence
- MIT
At a glance
Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook…
- Works in 6 steps: Merge files (CSV/Excel) → Analyze data (CSV/Excel) → Apply formulas (Excel only) → …
- Users ask to merge/clean tabular data
- SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 8 more sections
- Runs Python scripts from its folder; calls python
What it does
Spreadsheet Ops is an agent skill from aipoch/medical-research-skills. Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook recalculation.
Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 19 other files, including scripts and reference files (for example `POLISH_CHANGELOG.md`, `eval_report_spreadsheet-ops_result.json` and `references/analysis.md`).
It sits in Documents & Office, covering Excel spreadsheets. It works with Microsoft Excel and Python. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.
When your agent uses it
- Users ask to merge/clean tabular data
- Add/edit Excel formulas
- Apply formatting
- Generate charts
Example prompts
- “/spreadsheet-ops”
Requirements
- Python 3
Workflow steps
6 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 686e09d. 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 6 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Spreadsheet Ops loads about 1.7k tokens when it runs, and up to ~3k if it reads all its reference files. Until then it costs about 57 tokens; SKILL.md has 757 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
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 757 words, ~1,691 tokens.
Download SKILL.mdSave it as
.claude/skills/spreadsheet-ops/SKILL.md (or your agent's skills folder). This skill also uses 17 other files; get the full folder from GitHub.- name
- spreadsheet-ops
- description
- Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook recalculation.
- license
- MIT
- author
- AIPOCH
When to Use
- You need to merge multiple CSV/Excel files into a single dataset and align columns.
- You need to clean tabular data (normalize headers, deduplicate rows, resolve conflicts) before downstream use.
- You need to perform data analysis/statistics on CSV/Excel (summaries, distributions, group-by metrics).
- You need to add or edit formulas in an Excel workbook (including applying formulas across ranges).
- You need to apply Excel formatting (including conditional formatting), generate charts, or force formula recalculation.
Key Features
- CSV/Excel merge & cleaning: combine files, normalize column names, deduplicate, and resolve conflicts.
- CSV/Excel analysis: compute descriptive statistics and analysis reports.
- Excel-only formula operations: create/edit formulas and apply them to specified ranges.
- Excel-only formatting: apply cell styles and conditional formatting rules.
- Excel-only visualization: build charts from worksheet ranges.
- Excel-only recalculation: set workbook to full recalculation (recalc flag) to ensure formulas update.
Dependencies
- Python 3.x
- Project Python dependencies are defined by the repository environment (e.g.,
requirements.txt/ lockfile if present).
(No explicit versions were provided in the source document.)
Example Usage
The following commands assume you are in the repository root and have a Python environment available.
1) Merge files (CSV/Excel)
python scripts/merge_files.py2) Analyze data (CSV/Excel)
python scripts/analyze_data.py3) Apply formulas (Excel only)
python scripts/apply_formulas.py4) Apply formatting (Excel only)
python scripts/apply_formatting.py5) Build charts (Excel only)
python scripts/build_charts.py6) Force workbook recalculation (Excel only)
python scripts/recalc_workbook.pyImplementation Details
Workflow
- Confirm inputs/outputs: file paths, file formats (CSV vs Excel), worksheet names, and target ranges.
- Choose the task type: merge, analysis, formula, formatting, chart, or recalculation.
- Run the corresponding script and configure parameters in
CONFIG(as used by the scripts). - Produce output files and any generated reports.
Task boundaries
- CSV/Excel supported: merging/cleaning, data analysis.
- Excel only: formula creation/editing, formatting, chart visualization, and recalculation.
Key parameters to clarify (priority)
- Input type: CSV or Excel; single file or multiple files.
- Worksheet names and cell ranges to operate on (Excel).
- Whether formulas/formatting/charts must preserve original styles.
- Desired output format: CSV / Excel / JSON / Parquet.
Standards / constraints
- Python file I/O must explicitly specify
encoding='utf-8'. json.dump(...)must setensure_ascii=False.
- Python file I/O must explicitly specify
Reference documentation (optional)
- Column name matching & normalization:
references/column-matching.md - Deduplication & conflict resolution:
references/dedup-conflict.md - Large files & performance:
references/large-files.md - Formula design & ranges:
references/formulas.md - Formatting & conditional formatting:
references/formatting.md - Data analysis & statistics:
references/analysis.md - Charts & visualization:
references/visualization.md - Formula recalculation:
references/recalc.md
- Column name matching & normalization:
When Not to Use
- Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
- Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
- Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.
Show full SKILL.md (333 more words)Show less
Required Inputs
| Field | Required | Format/Source | Example | If Missing |
|---|---|---|---|---|
| User task description | Yes | Text | Research question, writing goal, analysis objective | Stop and ask user to provide |
| Primary input material | Depends on task | Text, file path, ID, table, or literature | PMID, PDF, CSV, DOCX, keywords, etc. | Specify which material type is missing |
| Output preference | No | Text | Language, format, target journal, template | Use skill default format |
Output Contract
- Primary output: Structured result or target file aligned with this skill's objective.
- Optional output: Intermediate check notes, issue list, supplementary suggestions, or generated file paths.
- Format requirement: Unless the user specifies otherwise, prefer stable, reviewable Markdown or JSON; if the skill's bundled script requires a fixed format, use that format.
- If partially complete: Must explicitly mark as PARTIAL and state which steps are completed and which remain.
Failure Handling
- Missing critical input: Explicitly state which fields, files, or identifiers are missing and pause.
- Script, template, or resource execution failure: Report the failing step, likely cause, and recovery suggestions — do not silently degrade.
- Partial completion only: Return the verified portion first, then list remaining blockers and suggested next steps.
User Checkpoints
- Before executing batch processing, overwriting files, long-running searches, or multi-stage generation, confirm scope and output format with the user.
- Before proceeding when a key judgment is ambiguous, evidence is insufficient, or the workflow is entering the next stage, confirm with the user.
Input Validation
This skill accepts requests that match the documented purpose of spreadsheet-ops and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
spreadsheet-opsonly handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
Quick Validation
- Check that key scripts, templates, or reference file paths this skill depends on exist.
- Check that the final output contains the core fields, sections, or files specified for this task.
- Check that results clearly mark assumptions, limitations, and incomplete items.
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 17 other files (scripts, references) in scientific-skills/Other/spreadsheet-ops of aipoch/medical-research-skills.
- SKILL.md
- POLISH_CHANGELOG.md
- eval_report_spreadsheet-ops_result.json
- references/analysis.md
- references/column-matching.md
- references/dedup-conflict.md
- references/formatting.md
- references/formulas.md
- references/large-files.md
- references/recalc.md
- references/report-template.md
- references/visualization.md
- scripts/analyze_data.py
- scripts/apply_formatting.py
- scripts/apply_formulas.py
- scripts/build_charts.py
- scripts/merge_files.py
- scripts/recalc_workbook.py
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Spreadsheet Ops 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 |
|---|---|---|---|---|---|---|
| Spreadsheet Ops this skillaipoch/medical-research-skills | 2k | — | ~1.7k | Automated safety check: Pass | MIT | |
| Instrument Data To Allotropeaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | 2 repos | ~2.7k | Automated safety check: Pass | Apache-2.0 | |
| Doc Cleanernotoriouslab/doc-cleaner | 309 | — | ~712 | Automated safety check: Pass | MIT | |
| MineruNebutra/MinerU-Skill | 122 | — | ~504 | Automated safety check: Pass | MIT | |
| XLSXzzhonglei/GeoCode-Release | 187 | — | ~3.1k | Automated safety check: Pass | MIT | |
| Python Bridgetmustier/pi-for-excel | 434 | — | ~820 | Automated safety check: Pass | MIT |
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Related
Works with
Categories
Questions about Spreadsheet Ops
What does Spreadsheet Ops do?
Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook…. Spreadsheet Ops is an agent skill from aipoch/medical-research-skills. Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook recalculation.
When should I use Spreadsheet Ops?
Spreadsheet Ops fits situations like: users ask to merge/clean tabular data; add/edit Excel formulas; apply formatting; generate charts.
How do I install Spreadsheet Ops in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill spreadsheet-ops -a claude-code`. Or copy the skill folder (scientific-skills/Other/spreadsheet-ops in aipoch/medical-research-skills) into .claude/skills/spreadsheet-ops in your project. Claude Code loads it when a task matches its description.
How do I install Spreadsheet Ops in Codex?
Run `npx skills add aipoch/medical-research-skills --skill spreadsheet-ops -a codex`. Or copy the skill folder (scientific-skills/Other/spreadsheet-ops in aipoch/medical-research-skills) into .agents/skills/spreadsheet-ops in your project. Codex loads it when a task matches its description.
Can I use Spreadsheet Ops 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 aipoch/medical-research-skills --skill spreadsheet-ops -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spreadsheet-ops, .gemini/skills/spreadsheet-ops, .github/skills/spreadsheet-ops and .opencode/skills/spreadsheet-ops in your project.
What does Spreadsheet Ops need to run?
Going by SKILL.md and its folder, Spreadsheet Ops needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Spreadsheet Ops access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Spreadsheet Ops 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 Spreadsheet Ops use?
Spreadsheet Ops is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Spreadsheet Ops use?
About 1.7k tokens (SKILL.md is roughly 6.8k 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 1.3k tokens, read only when the agent opens those files.
What are the alternatives to Spreadsheet Ops?
Skills that share tags, products or a category with Spreadsheet Ops: Instrument Data To Allotrope (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Doc Cleaner (notoriouslab/doc-cleaner, 309 stars), Mineru (Nebutra/MinerU-Skill, 122 stars) and XLSX (zzhonglei/GeoCode-Release, 187 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Spreadsheet Ops?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.
Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.