Gtars Genomic Interval Toolkit
davila7/claude-code-templates
Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.
The package comprises a set of pretrained machine learning models to predict basic immune cell types.
Install Bioconductor Scannotatr
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-scannotatr -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-scannotatr --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/scannotatr .claude/skills/bioconductor-scannotatr && 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-scannotatr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/scannotatr into .claude/skills/bioconductor-scannotatr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-scannotatr", 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/scannotatrType 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-scannotatr -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-scannotatr --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/scannotatr .agents/skills/bioconductor-scannotatr && 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-scannotatr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/scannotatr into .agents/skills/bioconductor-scannotatr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-scannotatr", 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-scannotatr -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-scannotatr --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/scannotatr .cursor/skills/bioconductor-scannotatr && 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-scannotatr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/scannotatr into .cursor/skills/bioconductor-scannotatr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-scannotatr", 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/scannotatr--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-scannotatr -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-scannotatr --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/scannotatr .gemini/skills/bioconductor-scannotatr && 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-scannotatr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/scannotatr into .gemini/skills/bioconductor-scannotatr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-scannotatr", 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-scannotatrInstalls 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-scannotatr -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/scannotatr .github/skills/bioconductor-scannotatr && 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-scannotatr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/scannotatr into .github/skills/bioconductor-scannotatr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-scannotatr", 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-scannotatr -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-scannotatr --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/scannotatr .opencode/skills/bioconductor-scannotatr && 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-scannotatr" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/scannotatr into .opencode/skills/bioconductor-scannotatr/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-scannotatr", 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-scannotatr- GitHub stars
- 804
- Token cost
- ~1.3k tokens
- SKILL.md length
- 389 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
The package comprises a set of pretrained machine learning models to predict basic immune cell types.
- 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 Machine learning
What it does
Bioconductor Scannotatr is an agent skill from bioMate-AI/biomate-bioconductor-kb. The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.
Its SKILL.md is about 1.3k 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 Machine learning. 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 Machine learning
Example prompts
- “/bioconductor-scannotatr”
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 Scannotatr loads about 1.3k tokens when it runs. Until then it costs about 94 tokens; SKILL.md has 389 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 389 words (~1,325 tokens).
“Train a new SVM classifier for an independent cell type and evaluate its performance.”
- name
- bioconductor-scannotatr
- when_to_use
- Use when: 1. Introduction to scAnnotatR; 2. Training basic model; 3. Training child model; Single-cell RNA-seq analysis (scAnnotatR). Not for: Requires R ≥…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/scannotatr of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Scannotatr 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 Scannotatr this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.3k | Automated safety check: Pass | Custom licence | |
| Gtars Genomic Interval Toolkitdavila7/claude-code-templates | 33k | 11 repos | ~1.9k | Automated safety check: Pass | MIT | |
| Bio Spatial Transcriptomics Spatial PreprocessingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| Bio Clip Seq M6a ClipGPTomics/bioSkills | 1.2k | 2 repos | ~5.7k | Automated safety check: Pass | MIT | |
| External Model Validationaipoch/medical-research-skills | 1.9k | — | ~3.2k | Automated safety check: Pass | MIT | |
| Bio Imaging Mass Cytometry Data PreprocessingGPTomics/bioSkills | 1.2k | 1 repos | ~4.2k | Automated safety check: Pass | MIT |
Similar skills
Bio Spatial Transcriptomics Spatial Preprocessing
FreedomIntelligence/OpenClaw-Medical-Skills
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data.
Bio Clip Seq M6a Clip
GPTomics/bioSkills
Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023, antibody-free chemical…
External Model Validation
aipoch/medical-research-skills
A skill your agent uses when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk…
Bio Imaging Mass Cytometry Data Preprocessing
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Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock…
Bio Temporal Genomics Temporal Grn
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Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives…
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Related
Categories
Questions about Bioconductor Scannotatr
What does Bioconductor Scannotatr do?
The package comprises a set of pretrained machine learning models to predict basic immune cell types. Bioconductor Scannotatr is an agent skill from bioMate-AI/biomate-bioconductor-kb. The package comprises a set of pretrained machine learning models to predict basic immune cell types.
When should I use Bioconductor Scannotatr?
Bioconductor Scannotatr fits situations like: tasks that involve Bioinformatics; tasks that involve Machine learning.
How do I install Bioconductor Scannotatr in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-scannotatr -a claude-code`. Or copy the skill folder (skills/transcriptomics/scannotatr in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-scannotatr in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Scannotatr in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-scannotatr -a codex`. Or copy the skill folder (skills/transcriptomics/scannotatr in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-scannotatr in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Scannotatr 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-scannotatr -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-scannotatr, .gemini/skills/bioconductor-scannotatr, .github/skills/bioconductor-scannotatr and .opencode/skills/bioconductor-scannotatr in your project.
What does Bioconductor Scannotatr need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Scannotatr is instructions for the agent only.
Does Bioconductor Scannotatr 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 Scannotatr 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 Scannotatr use?
Bioconductor Scannotatr 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 Scannotatr use?
About 1.3k tokens (SKILL.md is roughly 5.3k 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 Scannotatr?
Skills that share tags, products or a category with Bioconductor Scannotatr: Gtars Genomic Interval Toolkit (davila7/claude-code-templates, 33k stars), Bio Spatial Transcriptomics Spatial Preprocessing (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Clip Seq M6a Clip (GPTomics/bioSkills, 1.2k stars) and External Model Validation (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 Scannotatr?
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.