Bioinformatics Init Analysis

About this skill

Bioinformatics Init Analysis is a skill in LigphiDonk/Oh-my--paper (738 stars). Its SKILL.md is about 1.3k tokens, with 16 other files in the folder (scripts, references). Licence: MIT.

What it can do on your machine

Read from SKILL.md and the folder at commit 6baece9. 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 10 files in scripts/ (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python3
  • git
  • pip

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Hosts in commands or code, which the agent is likely to contact:

  • github.com

  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

Bioinformatics Init Analysis loads about 1.3k tokens when it runs, and up to ~7.2k if it reads all its reference files. Until then it costs about 15 tokens; SKILL.md has 287 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~15

When it runs · the whole SKILL.md, loaded when a task matches

~1.3k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~7.2k

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

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 LigphiDonk/Oh-my--paper at commit 6baece9, republished under its MIT licence (© LigphiDonk). 287 words, ~1,333 tokens.

name

bioinformatics-init-analysis

description

# bioinformatics-init-analysis

id

bioinformatics-init-analysis

version

1.0.0

stages

experiment

tools

read_file, search_project, write_file, run_terminal

summary

# bioinformatics-init-analysis

primaryIntent

research

intents

research

capabilities

research-planning, data-processing

domains

bioinformatics

keywords

bioinformatics-init-analysis, experiment

git clone https://github.com/<your-username>/bioinformatics-init-analysis.git \
    ~/.claude/plugins/bioinformatics-init-analysis

pip install scanpy anndata matplotlib seaborn scipy scikit-learn pandas numpy
# Optional: fcsparser (for .fcs flow cytometry files)

python3 scripts/run_pipeline.py <input_path> \
    [--data-type auto|cytof|scrnaseq|flow] \
    [--subsample 500] \
    [--output-dir ./analysis_output] \
    [--report-style clinical|technical]

# CyTOF directory of CSVs (auto-detected)
python3 scripts/run_pipeline.py /path/to/cytof_csvs/

# scRNA-seq h5ad file with technical report
python3 scripts/run_pipeline.py /path/to/data.h5ad --report-style technical

# Flow cytometry with more cells per sample
python3 scripts/run_pipeline.py /path/to/data.fcs --subsample 2000

analysis_output/
├── figures/                    # All generated plots (PNG)
├── processed/
│   └── adata_processed.h5ad   # Processed AnnData object
├── report.html                 # HTML report with embedded figures
└── analysis_summary.json       # Machine-readable summary statistics

bioinformatics-init-analysis/
├── .claude-plugin/
│   └── plugin.json             # Plugin manifest
├── skills/
│   └── init-analysis/
│       └── SKILL.md            # Skill definition (triggers, usage)
├── scripts/
│   ├── run_pipeline.py         # Main CLI entry point
│   ├── detect_data_type.py     # Auto-detection logic
│   ├── utils.py                # Shared utilities
│   ├── step1_load_data.py      # Universal data loader
│   ├── step2_qc.py             # Data-type-aware QC
│   ├── step3_normalize.py      # Normalization (arcsinh/CPM+log1p)
│   ├── step4_dim_reduction.py  # PCA + UMAP
│   ├── step5_clustering.py     # Leiden clustering + evaluation
│   ├── step6_marker_analysis.py# DE, correlation, treatment response
│   └── step7_report.py         # HTML report generator
├── references/
│   ├── plot_interpretation_guide.md  # How to read each plot type
│   ├── cytof_specifics.md            # CyTOF data handling
│   ├── scrnaseq_specifics.md         # scRNA-seq data handling
│   └── statistical_methods.md        # Stats glossary for non-experts
└── assets/                     # (reserved for future templates)

© LigphiDonk, 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 16 other files (scripts, references) in skills/bioinformatics-init-analysis of LigphiDonk/Oh-my--paper.

• SKILL.md
• README.md
• references/cytof_specifics.md
• references/plot_interpretation_guide.md
• references/scrnaseq_specifics.md
• references/statistical_methods.md
• scripts/detect_data_type.py
• scripts/run_pipeline.py
• scripts/step1_load_data.py
• scripts/step2_qc.py
• scripts/step3_normalize.py
• scripts/step4_dim_reduction.py
• scripts/step5_clustering.py
• scripts/step6_marker_analysis.py
• scripts/step7_report.py
• scripts/utils.py
• skills

Open the folder on GitHubat commit 6baece9