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.
A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique.
Install Bioconductor Screclassify
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-screclassify -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-screclassify --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/single-cell/screclassify .claude/skills/bioconductor-screclassify && 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-screclassify" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/single-cell/screclassify into .claude/skills/bioconductor-screclassify/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-screclassify", 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/single-cell/screclassifyType 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-screclassify -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-screclassify --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/single-cell/screclassify .agents/skills/bioconductor-screclassify && 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-screclassify" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/single-cell/screclassify into .agents/skills/bioconductor-screclassify/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-screclassify", 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-screclassify -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-screclassify --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/single-cell/screclassify .cursor/skills/bioconductor-screclassify && 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-screclassify" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/single-cell/screclassify into .cursor/skills/bioconductor-screclassify/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-screclassify", 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/single-cell/screclassify--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-screclassify -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-screclassify --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/single-cell/screclassify .gemini/skills/bioconductor-screclassify && 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-screclassify" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/single-cell/screclassify into .gemini/skills/bioconductor-screclassify/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-screclassify", 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-screclassifyInstalls 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-screclassify -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/single-cell/screclassify .github/skills/bioconductor-screclassify && 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-screclassify" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/single-cell/screclassify into .github/skills/bioconductor-screclassify/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-screclassify", 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-screclassify -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-screclassify --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/single-cell/screclassify .opencode/skills/bioconductor-screclassify && 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-screclassify" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/single-cell/screclassify into .opencode/skills/bioconductor-screclassify/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-screclassify", 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-screclassify- GitHub stars
- 804
- Token cost
- ~818 tokens
- SKILL.md length
- 289 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique.
- Tasks that involve Machine learning
- 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 Screclassify is an agent skill from bioMate-AI/biomate-bioconductor-kb. A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.
Its SKILL.md is about 820 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 Machine learning 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 Machine learning
- Tasks that involve Bioinformatics
Example prompts
- “/bioconductor-screclassify”
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
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
Bioconductor Screclassify loads about 818 tokens when it runs. Until then it costs about 81 tokens; SKILL.md has 289 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 289 words (~818 tokens).
“Correct and fine-tune noisy or mislabeled cell type annotations in single-cell RNA-seq data using semi-supervised learning.”
- name
- bioconductor-screclassify
- when_to_use
- Use when: An introduction to scReClassify package; Single-cell RNA-seq analysis (scReClassify). Not for: Requires R ≥ 4.1 and Bioconductor ≥ 3.16
- user-invocable
- false
Files
Just SKILL.md in skills/single-cell/screclassify of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Screclassify 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 Screclassify this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~818 | 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 |
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Related
Categories
Questions about Bioconductor Screclassify
What does Bioconductor Screclassify do?
A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. Bioconductor Screclassify is an agent skill from bioMate-AI/biomate-bioconductor-kb. A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique.
When should I use Bioconductor Screclassify?
Bioconductor Screclassify fits situations like: tasks that involve Machine learning; tasks that involve Bioinformatics.
How do I install Bioconductor Screclassify in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-screclassify -a claude-code`. Or copy the skill folder (skills/single-cell/screclassify in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-screclassify in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Screclassify in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-screclassify -a codex`. Or copy the skill folder (skills/single-cell/screclassify in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-screclassify in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Screclassify 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-screclassify -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-screclassify, .gemini/skills/bioconductor-screclassify, .github/skills/bioconductor-screclassify and .opencode/skills/bioconductor-screclassify in your project.
What does Bioconductor Screclassify need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Screclassify is instructions for the agent only.
Does Bioconductor Screclassify 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 Bioconductor Screclassify 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 Screclassify use?
Bioconductor Screclassify 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 Screclassify use?
About 818 tokens (SKILL.md is roughly 3.3k 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 Screclassify?
Skills that share tags, products or a category with Bioconductor Screclassify: 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 Screclassify?
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.