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.
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…
Install Gene Protein Expression Matrix Normalization
$ npx skills add aipoch/medical-research-skills --skill gene-protein-expression-matrix-normalization -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills gene-protein-expression-matrix-normalization --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/gene-protein-expression-matrix-normalization' .claude/skills/gene-protein-expression-matrix-normalization && 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 "gene-protein-expression-matrix-normalization" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gene-protein-expression-matrix-normalization into .claude/skills/gene-protein-expression-matrix-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gene-protein-expression-matrix-normalization", 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/gene-protein-expression-matrix-normalizationType 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 gene-protein-expression-matrix-normalization -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills gene-protein-expression-matrix-normalization --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/gene-protein-expression-matrix-normalization' .agents/skills/gene-protein-expression-matrix-normalization && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "gene-protein-expression-matrix-normalization" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gene-protein-expression-matrix-normalization into .agents/skills/gene-protein-expression-matrix-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gene-protein-expression-matrix-normalization", 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 gene-protein-expression-matrix-normalization -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills gene-protein-expression-matrix-normalization --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/gene-protein-expression-matrix-normalization' .cursor/skills/gene-protein-expression-matrix-normalization && 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 "gene-protein-expression-matrix-normalization" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gene-protein-expression-matrix-normalization into .cursor/skills/gene-protein-expression-matrix-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gene-protein-expression-matrix-normalization", 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/gene-protein-expression-matrix-normalization'--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 gene-protein-expression-matrix-normalization -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills gene-protein-expression-matrix-normalization --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/gene-protein-expression-matrix-normalization' .gemini/skills/gene-protein-expression-matrix-normalization && 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 "gene-protein-expression-matrix-normalization" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gene-protein-expression-matrix-normalization into .gemini/skills/gene-protein-expression-matrix-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gene-protein-expression-matrix-normalization", 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 gene-protein-expression-matrix-normalizationInstalls 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 gene-protein-expression-matrix-normalization -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/gene-protein-expression-matrix-normalization' .github/skills/gene-protein-expression-matrix-normalization && 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 "gene-protein-expression-matrix-normalization" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gene-protein-expression-matrix-normalization into .github/skills/gene-protein-expression-matrix-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gene-protein-expression-matrix-normalization", 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 gene-protein-expression-matrix-normalization -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 gene-protein-expression-matrix-normalization --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/gene-protein-expression-matrix-normalization' .opencode/skills/gene-protein-expression-matrix-normalization && 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 "gene-protein-expression-matrix-normalization" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/gene-protein-expression-matrix-normalization into .opencode/skills/gene-protein-expression-matrix-normalization/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gene-protein-expression-matrix-normalization", 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
gene-protein-expression-matrix-normalization- GitHub stars
- 2k
- Token cost
- ~1.5k tokens
- SKILL.md length
- 596 words
- Files
- 15 (incl. scripts, references)
- Skills in repo
- 578
- Repo updated
- First seen
- Licence
- MIT
At a glance
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…
- Normalizing bulk gene
- SKILL.md covers When to Use, When Not to Use, When to Read External Files and Usage, plus 6 more sections
- Runs R scripts from its folder
- Protein expression matrices with log2 transform
What it does
Gene Protein Expression Matrix Normalization is an agent skill from aipoch/medical-research-skills. Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 18 other files, including scripts and reference files (for example `eval_report_gene-protein-expression-matrix-normalization_result.json`, `references/algorithm.md` and `references/cli-guide.md`).
It sits in Research & Science, covering Database schema design and Bioinformatics. 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
- Normalizing bulk gene
- Protein expression matrices with log2 transform
- Z-score standardization
- Min-max scaling before downstream visualization
Example prompts
- “/gene-protein-expression-matrix-normalization”
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 7 files in scripts/ (R), which the agent can run.
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
Gene Protein Expression Matrix Normalization loads about 1.5k tokens when it runs, and up to ~2.9k if it reads all its reference files. Until then it costs about 86 tokens; SKILL.md has 596 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). 596 words, ~1,530 tokens.
Download SKILL.mdSave it as
.claude/skills/gene-protein-expression-matrix-normalization/SKILL.md (or your agent's skills folder). This skill also uses 14 other files; get the full folder from GitHub.- name
- gene-protein-expression-matrix-normalization
- description
- Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.
- license
- MIT
- author
- AIPOCH
Gene Protein Expression Matrix Normalization
When to Use
Use this skill when the user wants to normalize a numeric expression matrix before plotting, clustering, or exploratory comparison.
Typical requests:
- "Normalize this gene expression matrix with log2"
- "Do z-score scaling across samples"
- "Map protein abundance values into 0 to 1"
When Not to Use
Do not use this skill for:
- Count-model normalization such as CPM, TPM, TMM, or DESeq2 size factors
- Batch correction or covariate adjustment
- Single-cell preprocessing workflows
- Matrices that contain missing,
Inf, orNaNvalues unless they are cleaned first
When to Read External Files
When executing the analysis, run:
Rscript scripts/main.R --input_file <matrix.csv> --output_dir <output_dir> --method <log2|zscore|minmax>| Situation | File to Read | Purpose |
|---|---|---|
| Need to execute the workflow | scripts/main.R | CLI entry point |
| Need algorithm details | references/algorithm.md | Method definitions and assumptions |
| Encounter an error | references/troubleshooting.md | Standard error codes and fixes |
| Need examples or baseline run details | references/cli-guide.md | Ready-to-run commands and test record |
| Need dependency declarations | DESCRIPTION | Runtime package list |
Usage
Rscript scripts/main.R \
--input_file tests/data/expression_matrix.csv \
--output_dir ./output \
--method log2 \
--pseudo_count 1 \
--seed 42Arguments
| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-i | --input_file | file | required | Expression matrix in CSV or TSV format |
-o | --output_dir | dir | ./output | Output directory |
-m | --method | string | log2 | Normalization method: log2, zscore, minmax |
-r | --margin | string | column | Apply normalization by row or column |
-p | --pseudo_count | numeric | 1 | Added before log2 transformation |
-c | --center | boolean | true | Center values for z-score |
-s | --scale_values | boolean | true | Scale values for z-score |
-t | --timeout_seconds | integer | 0 | Optional timeout; 0 disables it |
-d | --delimiter | string | auto | Input delimiter: auto, csv, or tsv |
--seed | integer | 42 | Random seed | |
--verbose | boolean | true | Print progress logs |
Input Format
The first column must contain feature identifiers. Remaining columns must be finite numeric sample values.
Missing values and non-finite values such as NA, NaN, Inf, and -Inf are rejected.
feature,S1,S2,S3
TP53,10,20,30
EGFR,3,5,9This skill accepts gene or protein expression matrices. It does not infer count-model normalization such as CPM, TPM, TMM, or DESeq2 size factors.
Output Files
If --output_dir already exists, result files with the same names are overwritten. When --verbose=true, the workflow prints a warning before writing into a non-empty output directory.
For single-sample inputs, feature_summary.csv reports per-feature standard deviations as 0 by design because each feature contributes one observed value.
| File | Description |
|---|---|
table/normalized_matrix.csv | Normalized matrix with the original feature column preserved |
table/feature_summary.csv | Per-feature min, max, mean, and SD before and after normalization |
table/sample_summary.csv | Per-sample min, max, mean, and SD before and after normalization |
data/normalized_matrix.rds | Serialized normalized matrix and run metadata |
run_record.txt | Structured execution record |
output_manifest.txt | Output file manifest |
session_info.txt | R session information |
Show full SKILL.md (193 more words)Show less
Methods
log2
Computes log2(x + pseudo_count) for each numeric value.
zscore
Centers and scales along the selected margin. margin=column standardizes each sample; margin=row standardizes each feature.
When center=false and scale_values=true, the workflow divides by standard deviation without subtracting the mean first.
minmax
Rescales values to [0, 1] along the selected margin. Constant vectors are returned as zeros to avoid division-by-zero errors.
Error Handling
| Error | Cause | Solution |
|---|---|---|
SKILL_FILE_NOT_FOUND | Input file path is invalid | Check the input path |
SKILL_MISSING_COLUMNS | Matrix has fewer than two columns | Provide one feature column and at least one sample column |
SKILL_INVALID_PARAMETER | CLI value is unsupported or malformed, or the matrix contains non-finite values | Review the argument table and inspect the matrix values |
SKILL_TIMEOUT | The run exceeded --timeout_seconds | Increase the timeout or simplify the input size |
SKILL_EMPTY_DATA | No usable rows or columns remain | Check the input matrix |
Testing
Rscript scripts/main.R --help
Rscript tests/run_tests.R
Rscript tests/run_tests.R audit_output_check
Rscript tests/test_skill.R
Rscript tests/test_skill.R audit_output_check --skip-preparetests/run_tests.R executes bundled log2, zscore, and minmax runs and writes their outputs under tests/output/.
When you pass a relative directory name such as audit_output_check, the test runner writes outputs under tests/output/audit_output_check/.
Run tests/run_tests.R before tests/test_skill.R when you want to validate pre-generated outputs explicitly. The validation script can also prepare missing outputs on its own.
© 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 14 other files (scripts, references) in awesome-med-research-skills/Data Analysis/gene-protein-expression-matrix-normalization of aipoch/medical-research-skills.
- SKILL.md
- DESCRIPTION
- eval_report_gene-protein-expression-matrix-normalization_result.json
- references/algorithm.md
- references/cli-guide.md
- references/troubleshooting.md
- scripts/cli_options.R
- scripts/functions.R
- scripts/io.R
- scripts/main.R
- scripts/recording.R
- scripts/run_analysis.R
- scripts/utils.R
- tests/data/expression_matrix.csv
- tests/run_tests.R
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Gene Protein Expression Matrix Normalization 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 |
|---|---|---|---|---|---|---|
| Gene Protein Expression Matrix Normalization this skillaipoch/medical-research-skills | 2k | — | ~1.5k | Automated safety check: Pass | MIT | |
| 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 | |
| Bio Expression Matrix NormalizationGPTomics/bioSkills | 1.2k | 1 repos | ~6.2k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Gene Protein Expression Matrix Normalization
What does Gene Protein Expression Matrix Normalization do?
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…. Gene Protein Expression Matrix Normalization is an agent skill from aipoch/medical-research-skills. Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis.
When should I use Gene Protein Expression Matrix Normalization?
Gene Protein Expression Matrix Normalization fits situations like: normalizing bulk gene; protein expression matrices with log2 transform; Z-score standardization; min-max scaling before downstream visualization.
How do I install Gene Protein Expression Matrix Normalization in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill gene-protein-expression-matrix-normalization -a claude-code`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/gene-protein-expression-matrix-normalization in aipoch/medical-research-skills) into .claude/skills/gene-protein-expression-matrix-normalization in your project. Claude Code loads it when a task matches its description.
How do I install Gene Protein Expression Matrix Normalization in Codex?
Run `npx skills add aipoch/medical-research-skills --skill gene-protein-expression-matrix-normalization -a codex`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/gene-protein-expression-matrix-normalization in aipoch/medical-research-skills) into .agents/skills/gene-protein-expression-matrix-normalization in your project. Codex loads it when a task matches its description.
Can I use Gene Protein Expression Matrix Normalization 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 gene-protein-expression-matrix-normalization -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gene-protein-expression-matrix-normalization, .gemini/skills/gene-protein-expression-matrix-normalization, .github/skills/gene-protein-expression-matrix-normalization and .opencode/skills/gene-protein-expression-matrix-normalization in your project.
What does Gene Protein Expression Matrix Normalization need to run?
Going by SKILL.md and its folder, Gene Protein Expression Matrix Normalization needs R for the scripts in its folder.
Does Gene Protein Expression Matrix Normalization 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 Gene Protein Expression Matrix Normalization 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 Gene Protein Expression Matrix Normalization use?
Gene Protein Expression Matrix Normalization 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 Gene Protein Expression Matrix Normalization use?
About 1.5k tokens (SKILL.md is roughly 6.1k 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 Gene Protein Expression Matrix Normalization?
Skills that share tags, products or a category with Gene Protein Expression Matrix Normalization: Bio Chipseq Differential Binding (GPTomics/bioSkills, 1.2k stars), Bio Geo Data (GPTomics/bioSkills, 1.2k stars), Tooluniverse Metabolomics Analysis (wu-yc/LabClaw, 1.1k stars) and Bio Spatial Transcriptomics Spatial Preprocessing (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Gene Protein Expression Matrix Normalization?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,978 GitHub stars. The repository holds 578 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.