Exploratory Data Analysis
spacering-net/codeg
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval.
Install Bioconductor Matrixqcvis
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-matrixqcvis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-matrixqcvis --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/proteomics/matrixqcvis .claude/skills/bioconductor-matrixqcvis && 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-matrixqcvis" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/matrixqcvis into .claude/skills/bioconductor-matrixqcvis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-matrixqcvis", 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/proteomics/matrixqcvisType 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-matrixqcvis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-matrixqcvis --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/proteomics/matrixqcvis .agents/skills/bioconductor-matrixqcvis && 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-matrixqcvis" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/matrixqcvis into .agents/skills/bioconductor-matrixqcvis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-matrixqcvis", 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-matrixqcvis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-matrixqcvis --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/proteomics/matrixqcvis .cursor/skills/bioconductor-matrixqcvis && 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-matrixqcvis" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/matrixqcvis into .cursor/skills/bioconductor-matrixqcvis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-matrixqcvis", 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/proteomics/matrixqcvis--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-matrixqcvis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-matrixqcvis --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/proteomics/matrixqcvis .gemini/skills/bioconductor-matrixqcvis && 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-matrixqcvis" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/matrixqcvis into .gemini/skills/bioconductor-matrixqcvis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-matrixqcvis", 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-matrixqcvisInstalls 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-matrixqcvis -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/proteomics/matrixqcvis .github/skills/bioconductor-matrixqcvis && 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-matrixqcvis" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/matrixqcvis into .github/skills/bioconductor-matrixqcvis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-matrixqcvis", 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-matrixqcvis -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-matrixqcvis --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/proteomics/matrixqcvis .opencode/skills/bioconductor-matrixqcvis && 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-matrixqcvis" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/proteomics/matrixqcvis into .opencode/skills/bioconductor-matrixqcvis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-matrixqcvis", 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-matrixqcvis- GitHub stars
- 804
- Token cost
- ~1.1k tokens
- SKILL.md length
- 417 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval.
- Works in 12 steps: Samples measured/missing barplot → Feature missingness histogram → Feature missingness by condition → …
- 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
What it does
Bioconductor Matrixqcvis is an agent skill from bioMate-AI/biomate-bioconductor-kb. Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualiz
Its SKILL.md is about 1.1k 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, Bioinformatics and Data analysis. 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
- Tasks that involve Data analysis
Example prompts
- “/bioconductor-matrixqcvis”
Workflow steps
12 steps, taken from the first numbered list in SKILL.md.
- Samples measured/missing barplot
- Feature missingness histogram
- Feature missingness by condition
- UpSet plot of missingness across conditions
- Normalization
- Batch correction (default to none)
- Transformation (vsn with log2 fallback)
- Imputation (MinDet with minimum value fallback)
- CV comparison across processing stages
- Boxplot/Violin plot of processed values
- Drift Plot
- Distance Matrix Heatmap
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 Matrixqcvis loads about 1.1k tokens when it runs. Until then it costs about 131 tokens; SKILL.md has 417 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 417 words (~1,148 tokens).
“Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is…”
- name
- bioconductor-matrixqcvis
- when_to_use
- Use when: Shiny-based interactive data quality exploration of omics data; Metabolomics data analysis (MatrixQCvis); Proteomics quantification (MatrixQCvis)…
- user-invocable
- false
Files
Just SKILL.md in skills/proteomics/matrixqcvis of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Matrixqcvis 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 Matrixqcvis this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.1k | Automated safety check: Pass | Custom licence | |
| Exploratory Data Analysisspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Pass | MIT | |
| Pandas ProJeffallan/claude-skills | 12k | 1 repos | ~1.5k | Automated safety check: Pass | MIT | |
| Code EngineeropenJiuwen-ai/sciencediscovery | 162 | — | ~2.8k | Automated safety check: Pass | Apache-2.0 | |
| Verified Data Analysis with pandaspipeshub-ai/pipeshub-ai | 3.8k | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Exploratory Data Analysisminicoohei/ai-agent-camp | 347 | — | ~3.5k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Bioconductor Matrixqcvis
What does Bioconductor Matrixqcvis do?
Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. Bioconductor Matrixqcvis is an agent skill from bioMate-AI/biomate-bioconductor-kb. Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval.
When should I use Bioconductor Matrixqcvis?
Bioconductor Matrixqcvis fits situations like: tasks that involve Data cleaning; tasks that involve Bioinformatics; tasks that involve Data analysis.
How do I install Bioconductor Matrixqcvis in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-matrixqcvis -a claude-code`. Or copy the skill folder (skills/proteomics/matrixqcvis in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-matrixqcvis in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Matrixqcvis in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-matrixqcvis -a codex`. Or copy the skill folder (skills/proteomics/matrixqcvis in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-matrixqcvis in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Matrixqcvis 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-matrixqcvis -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-matrixqcvis, .gemini/skills/bioconductor-matrixqcvis, .github/skills/bioconductor-matrixqcvis and .opencode/skills/bioconductor-matrixqcvis in your project.
What does Bioconductor Matrixqcvis need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Matrixqcvis is instructions for the agent only.
Does Bioconductor Matrixqcvis 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 Matrixqcvis 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 Matrixqcvis use?
Bioconductor Matrixqcvis 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 Matrixqcvis use?
About 1.1k tokens (SKILL.md is roughly 4.6k 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 Matrixqcvis?
Skills that share tags, products or a category with Bioconductor Matrixqcvis: Exploratory Data Analysis (spacering-net/codeg, 3.9k stars), Pandas Pro (Jeffallan/claude-skills, 12k stars), Code Engineer (openJiuwen-ai/sciencediscovery, 162 stars) and Verified Data Analysis with pandas (pipeshub-ai/pipeshub-ai, 3.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Matrixqcvis?
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.