Deepspot M
K-Dense-AI/scientific-agent-skills
Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data.
Install Bioconductor Nnsvg
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nnsvg -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nnsvg --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/nnsvg .claude/skills/bioconductor-nnsvg && 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-nnsvg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nnsvg into .claude/skills/bioconductor-nnsvg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nnsvg", 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/nnsvgType 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-nnsvg -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nnsvg --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/nnsvg .agents/skills/bioconductor-nnsvg && 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-nnsvg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nnsvg into .agents/skills/bioconductor-nnsvg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nnsvg", 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-nnsvg -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nnsvg --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/nnsvg .cursor/skills/bioconductor-nnsvg && 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-nnsvg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nnsvg into .cursor/skills/bioconductor-nnsvg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nnsvg", 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/nnsvg--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-nnsvg -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-nnsvg --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/nnsvg .gemini/skills/bioconductor-nnsvg && 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-nnsvg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nnsvg into .gemini/skills/bioconductor-nnsvg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nnsvg", 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-nnsvgInstalls 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-nnsvg -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/nnsvg .github/skills/bioconductor-nnsvg && 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-nnsvg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nnsvg into .github/skills/bioconductor-nnsvg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nnsvg", 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-nnsvg -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-nnsvg --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/nnsvg .opencode/skills/bioconductor-nnsvg && 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-nnsvg" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/nnsvg into .opencode/skills/bioconductor-nnsvg/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-nnsvg", 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-nnsvg- GitHub stars
- 804
- Token cost
- ~925 tokens
- SKILL.md length
- 314 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data.
- 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 Slides and decks
What it does
Bioconductor Nnsvg is an agent skill from bioMate-AI/biomate-bioconductor-kb. Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more
Its SKILL.md is about 930 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 Slides and decks. 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 Slides and decks
Example prompts
- “/bioconductor-nnsvg”
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 Nnsvg loads about 925 tokens when it runs. Until then it costs about 130 tokens; SKILL.md has 314 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 314 words (~925 tokens).
“Input: A SpatialExperiment object containing raw counts and spatial coordinates. Output: A SpatialExperiment object with SVG ranking and statistics stored in rowData.”
- name
- bioconductor-nnsvg
- when_to_use
- Use when: Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data; Single-cell RNA-seq analysis…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/nnsvg of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Nnsvg 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 Nnsvg this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~925 | Automated safety check: Pass | Custom licence | |
| Deepspot MK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.5k | Automated safety check: Notes | PolyForm-Noncommercial-1.0.0 | |
| Single2spatial Spatial MappingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 2 repos | ~994 | Automated safety check: Pass | None | |
| Bio Spatial Transcriptomics Spatial Data IoFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| Bio Spatial Transcriptomics Spatial MultiomicsFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.6k | Automated safety check: Pass | None | |
| Bio Spatial Transcriptomics High Resolution BinningGPTomics/bioSkills | 1.2k | 1 repos | ~3.7k | Automated safety check: Pass | MIT |
Similar skills
Single2spatial Spatial Mapping
FreedomIntelligence/OpenClaw-Medical-Skills
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Bio Spatial Transcriptomics Spatial Data Io
FreedomIntelligence/OpenClaw-Medical-Skills
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
Bio Spatial Transcriptomics Spatial Multiomics
FreedomIntelligence/OpenClaw-Medical-Skills
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.
Bio Spatial Transcriptomics High Resolution Binning
GPTomics/bioSkills
Reconstructs single cells from sub-cellular spatial capture units (Visium HD 2um bins, Stereo-seq DNB spots, Slide-seqV2 beads) by aggregating bins UP into cells rather than deconvolving a mixture…
Bio Spatial Transcriptomics Spatial Domains
GPTomics/bioSkills
Identify spatially coherent tissue domains (regions like cortical layers, tumor vs stroma) in Visium, Visium HD, Xenium, MERFISH, Slide-seq, and Stereo-seq data with Squidpy, BANKSY, BayesSpace…
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Related
Categories
Questions about Bioconductor Nnsvg
What does Bioconductor Nnsvg do?
Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. Bioconductor Nnsvg is an agent skill from bioMate-AI/biomate-bioconductor-kb. Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data.
When should I use Bioconductor Nnsvg?
Bioconductor Nnsvg fits situations like: tasks that involve Bioinformatics; tasks that involve Slides and decks.
How do I install Bioconductor Nnsvg in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nnsvg -a claude-code`. Or copy the skill folder (skills/transcriptomics/nnsvg in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-nnsvg in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Nnsvg in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-nnsvg -a codex`. Or copy the skill folder (skills/transcriptomics/nnsvg in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-nnsvg in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Nnsvg 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-nnsvg -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-nnsvg, .gemini/skills/bioconductor-nnsvg, .github/skills/bioconductor-nnsvg and .opencode/skills/bioconductor-nnsvg in your project.
What does Bioconductor Nnsvg need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Nnsvg is instructions for the agent only.
Does Bioconductor Nnsvg 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 Nnsvg 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 Nnsvg use?
Bioconductor Nnsvg 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 Nnsvg use?
About 925 tokens (SKILL.md is roughly 3.7k 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 Nnsvg?
Skills that share tags, products or a category with Bioconductor Nnsvg: Deepspot M (K-Dense-AI/scientific-agent-skills, 48k stars), Single2spatial Spatial Mapping (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Spatial Transcriptomics Spatial Data Io (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars) and Bio Spatial Transcriptomics Spatial Multiomics (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Nnsvg?
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.