Excel and CSV Data Analysis
bytedance/deer-flow
Analyzes uploaded Excel and CSV files with SQL through DuckDB, producing schema inspections, statistical summaries and exports to CSV, JSON or Markdown.
A skill your agent uses when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status…
$ npx skills add aipoch/medical-research-skills --skill sample-group-sankey-plot -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills sample-group-sankey-plot --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/'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot' .claude/skills/sample-group-sankey-plot && 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 "sample-group-sankey-plot" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plot into .claude/skills/sample-group-sankey-plot/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sample-group-sankey-plot", 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/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plotType 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 sample-group-sankey-plot -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills sample-group-sankey-plot --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/'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot' .agents/skills/sample-group-sankey-plot && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "sample-group-sankey-plot" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plot into .agents/skills/sample-group-sankey-plot/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sample-group-sankey-plot", 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 sample-group-sankey-plot -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills sample-group-sankey-plot --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/'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot' .cursor/skills/sample-group-sankey-plot && 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 "sample-group-sankey-plot" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plot into .cursor/skills/sample-group-sankey-plot/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sample-group-sankey-plot", 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 'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot'--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 sample-group-sankey-plot -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills sample-group-sankey-plot --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/'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot' .gemini/skills/sample-group-sankey-plot && 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 "sample-group-sankey-plot" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plot into .gemini/skills/sample-group-sankey-plot/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sample-group-sankey-plot", 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 sample-group-sankey-plotInstalls 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 sample-group-sankey-plot -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/'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot' .github/skills/sample-group-sankey-plot && 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 "sample-group-sankey-plot" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plot into .github/skills/sample-group-sankey-plot/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sample-group-sankey-plot", 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 sample-group-sankey-plot -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 sample-group-sankey-plot --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/'awesome-med-research-skills/Data Analysis/sample-group-sankey-plot' .opencode/skills/sample-group-sankey-plot && 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 "sample-group-sankey-plot" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/sample-group-sankey-plot into .opencode/skills/sample-group-sankey-plot/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "sample-group-sankey-plot", 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.
sample-group-sankey-plotA skill your agent uses when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status…
Sample Group Sankey Plot is an agent skill from aipoch/medical-research-skills. Use when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status, subtype, or cohort labels. NOT for: gene network flow analysis, continuous-value trajectories, or graph-structured pathway visualization.
Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 15 other files, including scripts and reference files (for example `eval_report_sample-group-sankey-plot_result.json`, `references/algorithm.md` and `references/cli-guide.md`).
It sits in Data & Analytics. 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.
4 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.
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.
Ships 5 files in scripts/ (R), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Sample Group Sankey Plot loads about 2.4k tokens when it runs, and up to ~4k if it reads all its reference files. Until then it costs about 85 tokens; SKILL.md has 952 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.
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.
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 952 words, ~2,422 tokens.
.claude/skills/sample-group-sankey-plot/SKILL.md (or your agent's skills folder). This skill also uses 11 other files; get the full folder from GitHub.Builds a reproducible Sankey/alluvial visualization from a tabular sample annotation file and exports the selected annotations, lodes-format table, plot PDF, and session metadata.
This skill accepts: a sample annotation table in CSV or TSV format where rows are samples and selected columns are categorical stages (e.g., risk group, response status, subtype, cohort label). At least 2 stage columns are required.
If the user's request does not involve generating a Sankey or alluvial flow diagram from categorical sample annotations — for example, asking to visualize a gene regulatory network, plot continuous-value trajectories, analyze pathway flow, or process non-tabular data — do not proceed with the workflow. Instead respond:
"sample-group-sankey-plot is designed to generate Sankey/alluvial plots from categorical sample annotation tables. Your request appears to be outside this scope. Please provide a sample annotation table with at least 2 categorical stage columns, or use a more appropriate tool for gene network visualization or pathway analysis."
Readability guidance: Sankey plots are recommended for fewer than 8 unique values per stage and fewer than 5 stages total. For larger inputs, filter or aggregate categories before plotting to ensure readable output.
After a successful run, report to the caller:
Sankey plot generated successfully.
Stages plotted : <comma-separated stage column names>
Samples : <row count>
Output prefix : <output_prefix>
Outputs:
table/selected_annotations.csv
table/sankey_lodes.csv
plot/<output_prefix>.pdf
data/session_info.txt
Readability warnings (if any): <advisory messages or "none">If the script exits with a non-zero status, surface the SKILL_* error code and message verbatim. Do not attempt to continue or retry silently.
| Situation | File to Read | Purpose |
|---|---|---|
| Need to run analysis | scripts/main.R | Execute: Rscript scripts/main.R --input_file ... --output_dir ... |
| Need algorithm details | references/algorithm.md | Alluvial transformation logic, assumptions, and plotting choices |
| Encounter errors | references/troubleshooting.md | Common errors and solutions |
| Need CLI examples | references/cli-guide.md | Detailed CLI examples |
| Need test data | tests/data/ | Sample annotation tables for smoke tests and regression checks |
→ Reference files algorithm.md, troubleshooting.md, and cli-guide.md are in references/. If absent, rely on the Error Handling table below for common issues.
Install required R packages before the first run:
Rscript scripts/install_dependencies.RNote: install_dependencies.R installs from CRAN without version pinning. Tested with ggalluvial >= 0.12.5 and ggplot2 >= 3.4.0. For reproducible CI environments, consider using remotes::install_version().
Rscript scripts/main.R \
--input_file ./annotations.csv \
--output_dir ./output \
--columns risk,Responder \
--seed 42| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-i | --input_file | character | required | Input CSV/TSV annotation table |
-o | --output_dir | character | ./output/ | Output directory |
-c | --columns | character | all columns | Comma-separated stage columns to include in the plot. When omitted, all columns in the file are used as stages. |
-p | --output_prefix | character | sankey_plot | Prefix for generated output files (alphanumeric, dot, underscore, or hyphen characters only) |
--width | numeric | 7 | Plot width in inches | |
--height | numeric | 5 | Plot height in inches | |
--alpha | numeric | 0.5 | Flow transparency between 0 and 1 | |
--label_size | numeric | 4.5 | Stratum label size | |
--missing_label | character | Missing | Replacement label for blank or NA strata | |
--title | character | empty | Optional plot title | |
-s | --seed | integer | 42 | Random seed recorded for reproducibility |
--timeout | integer | 3600 | Maximum allowed elapsed runtime in seconds; use 0 to disable |
input_file)Delimited text file where rows represent samples and each selected column is a categorical stage shown in the Sankey plot.
SampleID,risk,Responder,Subtype
S1,High,Yes,Basal
S2,Low,No,LumA
S3,High,Yes,Basal
S4,Low,No,LumBRequirements:
--columns is omitted.NA values are replaced with --missing_label.| File | Description |
|---|---|
table/selected_annotations.csv | Filtered table containing only the plotted stage columns |
table/sankey_lodes.csv | Long-format lodes table used to build the Sankey plot |
plot/{output_prefix}.pdf | Sankey/alluvial plot as a PDF file; default filename is sankey_plot.pdf |
data/session_info.txt | R session information and runtime parameters |
| Column | Type | Description |
|---|---|---|
| stage columns | character | One column per plotted stage in original order |
| Column | Type | Description |
|---|---|---|
sample_id | character | Synthetic row identifier used as the alluvium key |
x | character | Stage name |
stratum | character | Category label for the stage |
sample_id identifier.ggalluvial::to_lodes_form().After column selection, the script emits log_warn advisories when:
"More than 5 stages selected; plot may be hard to read. Consider filtering.""Stage <name> has <n> unique values; consider aggregating for readability."These are advisory only — the script continues and produces the plot.
geom_flow() and geom_stratum().sessionInfo() and runtime arguments for reproducibility.Rscript scripts/main.R \
-i tests/data/sample_annotations.csv \
-o tests/output \
-c risk,ResponderRscript scripts/main.R \
-i tests/data/sample_annotations.csv \
-o tests/output_three_stage \
-c risk,Responder,Subtype \
--title "Risk to response transitions"Rscript scripts/main.R \
-i tests/data/minimal_annotations.csv \
-o tests/output_all_columns| Error | Cause | Solution |
|---|---|---|
SKILL_FILE_NOT_FOUND | Input file does not exist | Check --input_file |
SKILL_EMPTY_DATA | The input file has zero rows or fewer than 2 usable columns | Provide a non-empty table with at least 2 stage columns |
SKILL_MISSING_COLUMNS | A requested stage column is absent | Correct --columns or fix the input header |
SKILL_INVALID_PARAMETER | Width, height, alpha, label size, or output prefix is invalid | Provide valid arguments per the Arguments table |
SKILL_DEPENDENCY_MISSING | A required R package is unavailable | Run Rscript scripts/install_dependencies.R |
SKILL_IO_ERROR | Output directory cannot be created or written | Check permissions on --output_dir |
IF error persists, READ: references/troubleshooting.md
Rscript scripts/install_dependencies.R
Rscript scripts/main.R --help
Rscript scripts/main.R \
-i tests/data/sample_annotations.csv \
-o tests/output \
-c risk,Responder,Subtype
Rscript tests/test_skill.R
Rscript tests/run_smoke_test.Rls -la tests/output/table
ls -la tests/output/plot
ls -la tests/output/dataFor detailed algorithm, READ: references/algorithm.md
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 11 other files (scripts, references) in awesome-med-research-skills/Data Analysis/sample-group-sankey-plot of aipoch/medical-research-skills.
Open the folder on GitHubat commit 686e09d
Sample Group Sankey Plot 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 |
|---|---|---|---|---|---|---|
| Sample Group Sankey Plot this skillaipoch/medical-research-skills | 2k | — | ~2.4k | Automated safety check: Pass | MIT | |
| Excel and CSV Data Analysisbytedance/deer-flow | 83k | 4 repos | ~2.2k | Automated safety check: Pass | MIT | |
| Exploratory Data AnalysisOleafly/Oleafly | 206 | 3 repos | ~3.4k | Automated safety check: Notes | MIT | |
| CSV Data Summarizercoffeefuelbump/csv-data-summarizer-claude-skill | 468 | 2 repos | ~1.4k | Automated safety check: Pass | None | |
| Ieee Figure TableCloudWave818/ieee-skills | 355 | — | ~1k | Automated safety check: Pass | MIT | |
| Raccoon DataanalysisSenseTime-Copilot/raccoon-dataanalysis-skill | 137 | — | ~1.9k | Automated safety check: Pass | None |
bytedance/deer-flow
Analyzes uploaded Excel and CSV files with SQL through DuckDB, producing schema inspections, statistical summaries and exports to CSV, JSON or Markdown.
Oleafly/Oleafly
Perform bounded, local exploratory analysis of explicitly supported scientific files.
coffeefuelbump/csv-data-summarizer-claude-skill
Analyzes CSV files, generates summary stats, and plots quick visualizations using Python and pandas.
CloudWave818/ieee-skills
Audit, redesign, generate, and improve IEEE manuscript figures, tables, captions, result presentation, plotting scripts, visual polish, hybrid Python/R plus vector-editor workflows…
SenseTime-Copilot/raccoon-dataanalysis-skill
Raccoon (小浣熊) Data Analysis - Remote code interpreter and data visualization service powered by SenseTime.
ricardoherediaj/football-analytics-tutorials
Build post-match team + player reports (24-chart dashboard, per-player dashboards, stats CSV) from a WhoScored URL.
aipoch/medical-research-skills
Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster…
aipoch/medical-research-skills
Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.
aipoch/medical-research-skills
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
aipoch/medical-research-skills
A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS.
aipoch/medical-research-skills
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…
aipoch/medical-research-skills
Creates academic-poster writing packages for LaTeX using beamerposter, tikzposter, or baposter.
Categories
A skill your agent uses when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status…. Sample Group Sankey Plot is an agent skill from aipoch/medical-research-skills. Use when generating Sankey or alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group, response status, subtype, or cohort labels.
Sample Group Sankey Plot fits situations like: generating Sankey; alluvial plots from sample annotation tables where rows are samples and selected columns are categorical stages such as risk group; response status.
Run `npx skills add aipoch/medical-research-skills --skill sample-group-sankey-plot -a claude-code`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/sample-group-sankey-plot in aipoch/medical-research-skills) into .claude/skills/sample-group-sankey-plot in your project. Claude Code loads it when a task matches its description.
Run `npx skills add aipoch/medical-research-skills --skill sample-group-sankey-plot -a codex`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/sample-group-sankey-plot in aipoch/medical-research-skills) into .agents/skills/sample-group-sankey-plot in your project. Codex loads it when a task matches its description.
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 sample-group-sankey-plot -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/sample-group-sankey-plot, .gemini/skills/sample-group-sankey-plot, .github/skills/sample-group-sankey-plot and .opencode/skills/sample-group-sankey-plot in your project.
Going by SKILL.md and its folder, Sample Group Sankey Plot needs R for the scripts in its folder.
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.
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.
Sample Group Sankey Plot is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.4k tokens (SKILL.md is roughly 9.7k 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 1.6k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Sample Group Sankey Plot: Excel and CSV Data Analysis (bytedance/deer-flow, 83k stars), Exploratory Data Analysis (Oleafly/Oleafly, 206 stars), CSV Data Summarizer (coffeefuelbump/csv-data-summarizer-claude-skill, 468 stars) and Ieee Figure Table (CloudWave818/ieee-skills, 355 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
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.