Bio Machine Learning Atlas Mapping
GPTomics/bioSkills
Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with…
The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules.
Install Bioconductor Orfhunter
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-orfhunter -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-orfhunter --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/orfhunter .claude/skills/bioconductor-orfhunter && 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-orfhunter" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/orfhunter into .claude/skills/bioconductor-orfhunter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-orfhunter", 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/orfhunterType 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-orfhunter -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-orfhunter --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/orfhunter .agents/skills/bioconductor-orfhunter && 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-orfhunter" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/orfhunter into .agents/skills/bioconductor-orfhunter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-orfhunter", 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-orfhunter -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-orfhunter --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/orfhunter .cursor/skills/bioconductor-orfhunter && 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-orfhunter" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/orfhunter into .cursor/skills/bioconductor-orfhunter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-orfhunter", 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/orfhunter--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-orfhunter -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-orfhunter --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/orfhunter .gemini/skills/bioconductor-orfhunter && 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-orfhunter" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/orfhunter into .gemini/skills/bioconductor-orfhunter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-orfhunter", 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-orfhunterInstalls 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-orfhunter -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/orfhunter .github/skills/bioconductor-orfhunter && 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-orfhunter" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/orfhunter into .github/skills/bioconductor-orfhunter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-orfhunter", 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-orfhunter -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-orfhunter --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/orfhunter .opencode/skills/bioconductor-orfhunter && 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-orfhunter" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/orfhunter into .opencode/skills/bioconductor-orfhunter/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-orfhunter", 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-orfhunter- GitHub stars
- 804
- Token cost
- ~1.9k tokens
- SKILL.md length
- 511 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules.
- Tasks that involve Machine learning
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Reaches sstcenter.com
- Tasks that involve Bioinformatics
What it does
Bioconductor Orfhunter is an agent skill from bioMate-AI/biomate-bioconductor-kb. The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules fr
Its SKILL.md is about 1.9k 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 Machine learning and Bioinformatics. It works with C++. 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-orfhunter”
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
Hosts in commands or code, which the agent is likely to contact:
sstcenter.com
Also links to:
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 Orfhunter loads about 1.9k tokens when it runs. Until then it costs about 131 tokens; SKILL.md has 511 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 511 words (~1,921 tokens).
“Input: FASTA file of transcript sequences and a pre-trained Random Forest model. Output: Predicted ORFs, extracted sequences, PTC status, translated proteins, and a comprehensive annotation table.”
- name
- bioconductor-orfhunter
- when_to_use
- Use when: The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF); The ORFhunteR package…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/orfhunter of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Orfhunter 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 Orfhunter this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.9k | Automated safety check: Pass | Custom licence | |
| Bio Machine Learning Atlas MappingGPTomics/bioSkills | 1.2k | 1 repos | ~5.2k | Automated safety check: Pass | MIT | |
| Bio Microbiome Qiime2 WorkflowGPTomics/bioSkills | 1.2k | 1 repos | ~5.7k | Automated safety check: Pass | MIT | |
| Comorbidity Common Immune Biomarker Research Planneraipoch/medical-research-skills | 1.9k | — | ~4.5k | Automated safety check: Pass | MIT | |
| Process Related Diagnostic Biomarker Nomogram Research Planneraipoch/medical-research-skills | 1.9k | — | ~4.7k | Automated safety check: Pass | MIT | |
| Sap Hana Cloud Data Intelligencesecondsky/sap-skills | 462 | — | ~3.2k | Automated safety check: Pass | GPL-3.0 |
Similar skills
Bio Microbiome Qiime2 Workflow
GPTomics/bioSkills
Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality]…
Comorbidity Common Immune Biomarker Research Planner
aipoch/medical-research-skills
Generates complete comorbidity-oriented shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction.
Process Related Diagnostic Biomarker Nomogram Research Planner
aipoch/medical-research-skills
Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation direction.
Sap Hana Cloud Data Intelligence
secondsky/sap-skills
Develops data processing pipelines, integrations, and machine learning scenarios in SAP Data Intelligence Cloud.
Bio Microbiome Taxonomy Assignment
GPTomics/bioSkills
Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and primer region - DADA2 assignTaxonomy + addSpecies (RDP naive Bayes), DECIPHER IDTAXA…
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
Works with
Categories
Questions about Bioconductor Orfhunter
What does Bioconductor Orfhunter do?
The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. Bioconductor Orfhunter is an agent skill from bioMate-AI/biomate-bioconductor-kb. The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules.
When should I use Bioconductor Orfhunter?
Bioconductor Orfhunter fits situations like: tasks that involve Machine learning; tasks that involve Bioinformatics.
How do I install Bioconductor Orfhunter in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-orfhunter -a claude-code`. Or copy the skill folder (skills/transcriptomics/orfhunter in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-orfhunter in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Orfhunter in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-orfhunter -a codex`. Or copy the skill folder (skills/transcriptomics/orfhunter in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-orfhunter in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Orfhunter 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-orfhunter -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-orfhunter, .gemini/skills/bioconductor-orfhunter, .github/skills/bioconductor-orfhunter and .opencode/skills/bioconductor-orfhunter in your project.
What does Bioconductor Orfhunter need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Orfhunter is instructions for the agent only.
Does Bioconductor Orfhunter access the network?
SKILL.md names 2 domains. In commands or code: sstcenter.com; the agent is likely to contact it when it follows the instructions. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Orfhunter 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 Orfhunter use?
Bioconductor Orfhunter 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 Orfhunter use?
About 1.9k tokens (SKILL.md is roughly 7.7k 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 Orfhunter?
Skills that share tags, products or a category with Bioconductor Orfhunter: Bio Machine Learning Atlas Mapping (GPTomics/bioSkills, 1.2k stars), Bio Microbiome Qiime2 Workflow (GPTomics/bioSkills, 1.2k stars), Comorbidity Common Immune Biomarker Research Planner (aipoch/medical-research-skills, 1.9k stars) and Process Related Diagnostic Biomarker Nomogram Research Planner (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 Orfhunter?
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.