Bio Long Read Splicing
GPTomics/bioSkills
Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution.
SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks.
Install Bioconductor Sgcp
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-sgcp -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-sgcp --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/sgcp .claude/skills/bioconductor-sgcp && 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-sgcp" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/sgcp into .claude/skills/bioconductor-sgcp/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-sgcp", 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/sgcpType 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-sgcp -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-sgcp --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/sgcp .agents/skills/bioconductor-sgcp && 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-sgcp" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/sgcp into .agents/skills/bioconductor-sgcp/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-sgcp", 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-sgcp -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-sgcp --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/sgcp .cursor/skills/bioconductor-sgcp && 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-sgcp" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/sgcp into .cursor/skills/bioconductor-sgcp/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-sgcp", 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/sgcp--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-sgcp -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-sgcp --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/sgcp .gemini/skills/bioconductor-sgcp && 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-sgcp" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/sgcp into .gemini/skills/bioconductor-sgcp/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-sgcp", 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-sgcpInstalls 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-sgcp -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/sgcp .github/skills/bioconductor-sgcp && 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-sgcp" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/sgcp into .github/skills/bioconductor-sgcp/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-sgcp", 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-sgcp -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-sgcp --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/sgcp .opencode/skills/bioconductor-sgcp && 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-sgcp" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/sgcp into .opencode/skills/bioconductor-sgcp/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-sgcp", 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-sgcp- GitHub stars
- 804
- Token cost
- ~1.5k tokens
- SKILL.md length
- 548 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks.
- 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 Creative writing and fiction
What it does
Bioconductor Sgcp is an agent skill from bioMate-AI/biomate-bioconductor-kb. SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.
Its SKILL.md is about 1.5k 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 Creative writing and fiction. 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 Creative writing and fiction
Example prompts
- “/bioconductor-sgcp”
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 Sgcp loads about 1.5k tokens when it runs. Until then it costs about 109 tokens; SKILL.md has 548 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 548 words (~1,529 tokens).
“Construct gene co-expression networks, perform clustering, and apply semi-supervised classification using Gene Ontology information.”
- name
- bioconductor-sgcp
- when_to_use
- Use when: SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks; SGCP package manual. Not for: Requires R ≥ 4.2.0 and…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/sgcp of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Sgcp 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 Sgcp this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Bio Long Read SplicingGPTomics/bioSkills | 1.2k | 2 repos | ~6k | Automated safety check: Pass | MIT | |
| Bio Splicing QcGPTomics/bioSkills | 1.2k | 2 repos | ~6.2k | Automated safety check: Pass | MIT | |
| Bio Workflows Smrna PipelineGPTomics/bioSkills | 1.2k | 1 repos | ~3.8k | Automated safety check: Pass | MIT | |
| Popv Cell Annotationjaechang-hits/SciAgent-Skills | 374 | 2 repos | ~6.9k | Automated safety check: Pass | BSD-3-Clause | |
| Bio Long Read Sequencing Isoseq AnalysisGPTomics/bioSkills | 1.2k | 1 repos | ~3.4k | Automated safety check: Pass | MIT |
Similar skills
Bio Splicing Qc
GPTomics/bioSkills
Assesses RNA-seq data quality specifically for alternative splicing analysis.
Bio Workflows Smrna Pipeline
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Orchestrates the end-to-end small RNA-seq pipeline from FASTQ to differential miRNAs and expression-filtered targets, chaining kit-aware cutadapt trimming (adapter on every read, UMI/4N handling)…
Popv Cell Annotation
jaechang-hits/SciAgent-Skills
Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via…
Bio Long Read Sequencing Isoseq Analysis
GPTomics/bioSkills
Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline…
Ccf Idea Optimizer
mikubaka88/CCFA-Skills
Develop and optimize rough CCF research ideas into problems, insights, mechanisms, and evidence plans.
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Related
Categories
Questions about Bioconductor Sgcp
What does Bioconductor Sgcp do?
SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. Bioconductor Sgcp is an agent skill from bioMate-AI/biomate-bioconductor-kb. SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks.
When should I use Bioconductor Sgcp?
Bioconductor Sgcp fits situations like: tasks that involve Bioinformatics; tasks that involve Creative writing and fiction.
How do I install Bioconductor Sgcp in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-sgcp -a claude-code`. Or copy the skill folder (skills/transcriptomics/sgcp in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-sgcp in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Sgcp in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-sgcp -a codex`. Or copy the skill folder (skills/transcriptomics/sgcp in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-sgcp in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Sgcp 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-sgcp -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-sgcp, .gemini/skills/bioconductor-sgcp, .github/skills/bioconductor-sgcp and .opencode/skills/bioconductor-sgcp in your project.
What does Bioconductor Sgcp need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Sgcp is instructions for the agent only.
Does Bioconductor Sgcp 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 Sgcp 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 Sgcp use?
Bioconductor Sgcp 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 Sgcp use?
About 1.5k tokens (SKILL.md is roughly 6.1k 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 Sgcp?
Skills that share tags, products or a category with Bioconductor Sgcp: Bio Long Read Splicing (GPTomics/bioSkills, 1.2k stars), Bio Splicing Qc (GPTomics/bioSkills, 1.2k stars), Bio Workflows Smrna Pipeline (GPTomics/bioSkills, 1.2k stars) and Popv Cell Annotation (jaechang-hits/SciAgent-Skills, 374 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Sgcp?
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.