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.
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data.
Install Bioconductor Spotclean
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-spotclean -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-spotclean --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/spotclean .claude/skills/bioconductor-spotclean && 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-spotclean" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/spotclean into .claude/skills/bioconductor-spotclean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-spotclean", 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/spotcleanType 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-spotclean -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-spotclean --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/spotclean .agents/skills/bioconductor-spotclean && 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-spotclean" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/spotclean into .agents/skills/bioconductor-spotclean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-spotclean", 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-spotclean -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-spotclean --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/spotclean .cursor/skills/bioconductor-spotclean && 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-spotclean" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/spotclean into .cursor/skills/bioconductor-spotclean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-spotclean", 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/spotclean--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-spotclean -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-spotclean --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/spotclean .gemini/skills/bioconductor-spotclean && 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-spotclean" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/spotclean into .gemini/skills/bioconductor-spotclean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-spotclean", 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-spotcleanInstalls 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-spotclean -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/spotclean .github/skills/bioconductor-spotclean && 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-spotclean" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/spotclean into .github/skills/bioconductor-spotclean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-spotclean", 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-spotclean -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-spotclean --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/spotclean .opencode/skills/bioconductor-spotclean && 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-spotclean" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/spotclean into .opencode/skills/bioconductor-spotclean/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-spotclean", 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-spotclean- GitHub stars
- 804
- Token cost
- ~1.5k tokens
- SKILL.md length
- 449 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
SpotClean is a computational method to adjust for spot swapping in spatial 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 Spotclean is an agent skill from bioMate-AI/biomate-bioconductor-kb. SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontamin
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 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-spotclean”
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):
doi.orgbioconductor.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 Spotclean loads about 1.5k tokens when it runs. Until then it costs about 131 tokens; SKILL.md has 449 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 449 words (~1,476 tokens).
“Load raw 10x Visium Space Ranger output, perform decontamination, visualize results, and convert to a Seurat object.”
- name
- bioconductor-spotclean
- when_to_use
- Use when: SpotClean; Single-cell RNA-seq analysis (SpotClean). Not for: Requires R ≥ 4.2.0 and Bioconductor ≥ 3.16
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/spotclean of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Spotclean 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 Spotclean this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Single2spatial Spatial MappingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 2 repos | ~994 | Automated safety check: Pass | None | |
| Bio Spatial Transcriptomics Spatial MultiomicsFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.6k | Automated safety check: Pass | None | |
| Pathmldavila7/claude-code-templates | 33k | 11 repos | ~1.9k | Automated safety check: Pass | MIT | |
| Deepspot MK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.5k | Automated safety check: Notes | PolyForm-Noncommercial-1.0.0 | |
| Bio Spatial Transcriptomics Spatial Data IoFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None |
Similar skills
Bio Spatial Transcriptomics Spatial Multiomics
FreedomIntelligence/OpenClaw-Medical-Skills
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.
Pathml
davila7/claude-code-templates
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data.
Deepspot M
K-Dense-AI/scientific-agent-skills
Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.
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 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…
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Related
Categories
Questions about Bioconductor Spotclean
What does Bioconductor Spotclean do?
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Bioconductor Spotclean is an agent skill from bioMate-AI/biomate-bioconductor-kb. SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data.
When should I use Bioconductor Spotclean?
Bioconductor Spotclean fits situations like: tasks that involve Bioinformatics; tasks that involve Slides and decks.
How do I install Bioconductor Spotclean in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-spotclean -a claude-code`. Or copy the skill folder (skills/transcriptomics/spotclean in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-spotclean in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Spotclean in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-spotclean -a codex`. Or copy the skill folder (skills/transcriptomics/spotclean in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-spotclean in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Spotclean 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-spotclean -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-spotclean, .gemini/skills/bioconductor-spotclean, .github/skills/bioconductor-spotclean and .opencode/skills/bioconductor-spotclean in your project.
What does Bioconductor Spotclean need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Spotclean is instructions for the agent only.
Does Bioconductor Spotclean access the network?
SKILL.md names 2 domains. As links in the text: doi.org and bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Spotclean 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 Spotclean use?
Bioconductor Spotclean 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 Spotclean use?
About 1.5k tokens (SKILL.md is roughly 5.9k 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 Spotclean?
Skills that share tags, products or a category with Bioconductor Spotclean: Single2spatial Spatial Mapping (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Spatial Transcriptomics Spatial Multiomics (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Pathml (davila7/claude-code-templates, 33k stars) and Deepspot M (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Spotclean?
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.