PyDESeq2 Differential Expression
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis.
Install Bioconductor Mirtarrnaseq
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mirtarrnaseq -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-mirtarrnaseq --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/mirtarrnaseq .claude/skills/bioconductor-mirtarrnaseq && 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-mirtarrnaseq" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/mirtarrnaseq into .claude/skills/bioconductor-mirtarrnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-mirtarrnaseq", 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/mirtarrnaseqType 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-mirtarrnaseq -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-mirtarrnaseq --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/mirtarrnaseq .agents/skills/bioconductor-mirtarrnaseq && 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-mirtarrnaseq" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/mirtarrnaseq into .agents/skills/bioconductor-mirtarrnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-mirtarrnaseq", 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-mirtarrnaseq -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-mirtarrnaseq --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/mirtarrnaseq .cursor/skills/bioconductor-mirtarrnaseq && 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-mirtarrnaseq" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/mirtarrnaseq into .cursor/skills/bioconductor-mirtarrnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-mirtarrnaseq", 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/mirtarrnaseq--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-mirtarrnaseq -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-mirtarrnaseq --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/mirtarrnaseq .gemini/skills/bioconductor-mirtarrnaseq && 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-mirtarrnaseq" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/mirtarrnaseq into .gemini/skills/bioconductor-mirtarrnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-mirtarrnaseq", 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-mirtarrnaseqInstalls 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-mirtarrnaseq -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/mirtarrnaseq .github/skills/bioconductor-mirtarrnaseq && 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-mirtarrnaseq" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/mirtarrnaseq into .github/skills/bioconductor-mirtarrnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-mirtarrnaseq", 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-mirtarrnaseq -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-mirtarrnaseq --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/mirtarrnaseq .opencode/skills/bioconductor-mirtarrnaseq && 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-mirtarrnaseq" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/mirtarrnaseq into .opencode/skills/bioconductor-mirtarrnaseq/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-mirtarrnaseq", 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-mirtarrnaseq- GitHub stars
- 804
- Token cost
- ~2k tokens
- SKILL.md length
- 509 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis.
- Tasks that involve Bioinformatics
- 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 Statistics
What it does
Bioconductor Mirtarrnaseq is an agent skill from bioMate-AI/biomate-bioconductor-kb. mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.
Its SKILL.md is about 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 Research & Science, covering Bioinformatics and Statistics. 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 Bioinformatics
- Tasks that involve Statistics
Example prompts
- “/bioconductor-mirtarrnaseq”
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 Mirtarrnaseq loads about 2k tokens when it runs. Until then it costs about 111 tokens; SKILL.md has 509 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 509 words (~1,959 tokens).
“Identify significant miRNA-mRNA correlations across three or more time points using fold change data and background distribution comparisons.”
- name
- bioconductor-mirtarrnaseq
- when_to_use
- Use when: mirTarRnaSeq; Differential expression analysis (mirTarRnaSeq). Not for: Requires R ≥ 4.1.0 and Bioconductor ≥ 3.16
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/mirtarrnaseq of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Mirtarrnaseq 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 Mirtarrnaseq this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~2k | Automated safety check: Pass | Custom licence | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT | |
| Ukb Ppp Region FetchClawBio/ClawBio | 1.2k | — | ~4.6k | Automated safety check: Pass | MIT | |
| TiledbvcfK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Volcano Plot Scriptaipoch/medical-research-skills | 1.9k | — | ~2.5k | Automated safety check: Pass | MIT | |
| Tooluniverse Epigenomicswu-yc/LabClaw | 1.1k | 2 repos | ~14k | Automated safety check: Pass | None |
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Production-ready genomics and epigenomics data processing for BixBench questions.
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Related
Categories
Questions about Bioconductor Mirtarrnaseq
What does Bioconductor Mirtarrnaseq do?
mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. Bioconductor Mirtarrnaseq is an agent skill from bioMate-AI/biomate-bioconductor-kb. mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis.
When should I use Bioconductor Mirtarrnaseq?
Bioconductor Mirtarrnaseq fits situations like: tasks that involve Bioinformatics; tasks that involve Statistics.
How do I install Bioconductor Mirtarrnaseq in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mirtarrnaseq -a claude-code`. Or copy the skill folder (skills/transcriptomics/mirtarrnaseq in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-mirtarrnaseq in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Mirtarrnaseq in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mirtarrnaseq -a codex`. Or copy the skill folder (skills/transcriptomics/mirtarrnaseq in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-mirtarrnaseq in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Mirtarrnaseq 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-mirtarrnaseq -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-mirtarrnaseq, .gemini/skills/bioconductor-mirtarrnaseq, .github/skills/bioconductor-mirtarrnaseq and .opencode/skills/bioconductor-mirtarrnaseq in your project.
What does Bioconductor Mirtarrnaseq need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Mirtarrnaseq is instructions for the agent only.
Does Bioconductor Mirtarrnaseq 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 Mirtarrnaseq 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 Mirtarrnaseq use?
Bioconductor Mirtarrnaseq 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 Mirtarrnaseq use?
About 2k tokens (SKILL.md is roughly 7.8k 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 Mirtarrnaseq?
Skills that share tags, products or a category with Bioconductor Mirtarrnaseq: PyDESeq2 Differential Expression (davila7/claude-code-templates, 33k stars), Ukb Ppp Region Fetch (ClawBio/ClawBio, 1.2k stars), Tiledbvcf (K-Dense-AI/scientific-agent-skills, 48k stars) and Volcano Plot Script (aipoch/medical-research-skills, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Mirtarrnaseq?
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.