Bio Proteomics Proteomics Qc
FreedomIntelligence/OpenClaw-Medical-Skills
Quality control and assessment for proteomics data. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma.
Install Bioconductor Harmonizr
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-harmonizr --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/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/transcriptomics/harmonizr .claude/skills/bioconductor-harmonizr && 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 "bioconductor-harmonizr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizr into .claude/skills/bioconductor-harmonizr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-harmonizr", 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/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizrType 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-harmonizr --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/transcriptomics/harmonizr .agents/skills/bioconductor-harmonizr && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bioconductor-harmonizr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizr into .agents/skills/bioconductor-harmonizr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-harmonizr", 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-harmonizr --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/transcriptomics/harmonizr .cursor/skills/bioconductor-harmonizr && 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 "bioconductor-harmonizr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizr into .cursor/skills/bioconductor-harmonizr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-harmonizr", 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/bioMate-AI/biomate-bioconductor-kb.git --path skills/transcriptomics/harmonizr--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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-harmonizr --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/transcriptomics/harmonizr .gemini/skills/bioconductor-harmonizr && 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 "bioconductor-harmonizr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizr into .gemini/skills/bioconductor-harmonizr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-harmonizr", 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 bioMate-AI/biomate-bioconductor-kb bioconductor-harmonizrInstalls 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/transcriptomics/harmonizr .github/skills/bioconductor-harmonizr && 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 "bioconductor-harmonizr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizr into .github/skills/bioconductor-harmonizr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-harmonizr", 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-harmonizr --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/transcriptomics/harmonizr .opencode/skills/bioconductor-harmonizr && 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 "bioconductor-harmonizr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/harmonizr into .opencode/skills/bioconductor-harmonizr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-harmonizr", 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
bioconductor-harmonizr- GitHub stars
- 804
- Token cost
- ~1.2k tokens
- SKILL.md length
- 450 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma.
- Tasks that involve Data cleaning
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Tasks that involve Bioinformatics
What it does
Bioconductor Harmonizr is an agent skill from bioMate-AI/biomate-bioconductor-kb. An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Data & Analytics, covering Data cleaning and Bioinformatics. The repository describes itself as: BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes.
When your agent uses it
- Tasks that involve Data cleaning
- Tasks that involve Bioinformatics
Example prompts
- “/bioconductor-harmonizr”
What it can do on your machine
Read from SKILL.md and the folder at commit c9bd4d8. 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
No scripts in the folder and no shell commands in SKILL.md (its code samples are r).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
bioconductor.org
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
Bioconductor Harmonizr loads about 1.2k tokens when it runs. Until then it costs about 117 tokens; SKILL.md has 450 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); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 450 words (~1,192 tokens).
“Perform batch effect correction on a data frame containing missing values using ComBat or limma.”
- name
- bioconductor-harmonizr
- when_to_use
- Use when: An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma; HarmonizR_Vignette. Not for…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/harmonizr of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Harmonizr 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 |
|---|---|---|---|---|---|---|
| Bioconductor Harmonizr this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.2k | Automated safety check: Pass | Custom licence | |
| Bio Proteomics Proteomics QcFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.8k | Automated safety check: Pass | None | |
| Bio Workflows Methylation PipelineGPTomics/bioSkills | 1.2k | 1 repos | ~3.7k | Automated safety check: Pass | MIT | |
| Bio Proteomics Differential AbundanceGPTomics/bioSkills | 1.2k | 1 repos | ~5.7k | Automated safety check: Pass | MIT | |
| Bio Chipseq QcFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~2.7k | Automated safety check: Pass | None | |
| Bio Splicing QcFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~1.6k | Automated safety check: Pass | None |
Similar skills
Bio Workflows Methylation Pipeline
GPTomics/bioSkills
Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation…
Bio Proteomics Differential Abundance
GPTomics/bioSkills
Tests for differentially abundant proteins between conditions with limma/DEqMS empirical-Bayes moderation, proDA/msqrob2/MSstats missingness modeling, and Python Welch+BH alternatives.
Bio Chipseq Qc
FreedomIntelligence/OpenClaw-Medical-Skills
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate…
Bio Splicing Qc
FreedomIntelligence/OpenClaw-Medical-Skills
Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC.
Bio Alignment Validation
GPTomics/bioSkills
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.
More from bioMate-AI/biomate-bioconductor-kb
All 112 skills in this repoBioconductor Annotationhub
bioMate-AI/biomate-bioconductor-kb
This package provides a client for the Bioconductor AnnotationHub web resource.
Bioconductor Asurat
bioMate-AI/biomate-bioconductor-kb
ASURAT is a software for single-cell data analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.
Bioconductor Awst
bioMate-AI/biomate-bioconductor-kb
We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples.
Bioconductor Bandle
bioMate-AI/biomate-bioconductor-kb
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
Bioconductor Batchelor
bioMate-AI/biomate-bioconductor-kb
Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
Bioconductor Beer
bioMate-AI/biomate-bioconductor-kb
BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.
Related
Categories
Questions about Bioconductor Harmonizr
What does Bioconductor Harmonizr do?
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. Bioconductor Harmonizr is an agent skill from bioMate-AI/biomate-bioconductor-kb. An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma.
When should I use Bioconductor Harmonizr?
Bioconductor Harmonizr fits situations like: tasks that involve Data cleaning; tasks that involve Bioinformatics.
How do I install Bioconductor Harmonizr in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a claude-code`. Or copy the skill folder (skills/transcriptomics/harmonizr in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-harmonizr in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Harmonizr in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a codex`. Or copy the skill folder (skills/transcriptomics/harmonizr in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-harmonizr in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Harmonizr 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-harmonizr -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bioconductor-harmonizr, .gemini/skills/bioconductor-harmonizr, .github/skills/bioconductor-harmonizr and .opencode/skills/bioconductor-harmonizr in your project.
What does Bioconductor Harmonizr need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Harmonizr is instructions for the agent only.
Does Bioconductor Harmonizr access the network?
SKILL.md names 1 domain. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Harmonizr 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. Review the folder before installing.
What licence does Bioconductor Harmonizr use?
Bioconductor Harmonizr has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Bioconductor Harmonizr use?
About 1.2k tokens (SKILL.md is roughly 4.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bioconductor Harmonizr?
Skills that share tags, products or a category with Bioconductor Harmonizr: Bio Proteomics Proteomics Qc (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Workflows Methylation Pipeline (GPTomics/bioSkills, 1.2k stars), Bio Proteomics Differential Abundance (GPTomics/bioSkills, 1.2k stars) and Bio Chipseq Qc (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 Bioconductor Harmonizr?
bioMate-AI (a GitHub organization) maintains it in bioMate-AI/biomate-bioconductor-kb, which has 804 GitHub stars. The repository holds 112 skills in this directory. The repository was last updated on June 20, 2026.
Source: bioMate-AI/biomate-bioconductor-kb on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.