tangermeme Genomic Model Analysis
jmschrei/tangermeme
Routes agents to the right tangermeme reference for analyzing trained genomic deep learning models, from attributions and motif experiments to variant effects and design.
This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input.
Install Bioconductor Easier
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-easier -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-easier --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/easier .claude/skills/bioconductor-easier && 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-easier" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/easier into .claude/skills/bioconductor-easier/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-easier", 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/easierType 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-easier -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-easier --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/easier .agents/skills/bioconductor-easier && 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-easier" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/easier into .agents/skills/bioconductor-easier/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-easier", 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-easier -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-easier --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/easier .cursor/skills/bioconductor-easier && 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-easier" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/easier into .cursor/skills/bioconductor-easier/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-easier", 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/easier--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-easier -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-easier --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/easier .gemini/skills/bioconductor-easier && 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-easier" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/easier into .gemini/skills/bioconductor-easier/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-easier", 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-easierInstalls 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-easier -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/easier .github/skills/bioconductor-easier && 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-easier" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/easier into .github/skills/bioconductor-easier/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-easier", 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-easier -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-easier --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/easier .opencode/skills/bioconductor-easier && 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-easier" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/easier into .opencode/skills/bioconductor-easier/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-easier", 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-easier- GitHub stars
- 804
- Token cost
- ~1.9k tokens
- SKILL.md length
- 535 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input.
- 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 Machine learning
What it does
Bioconductor Easier is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in
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 Research & Science, covering Bioinformatics and Machine learning. 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 Machine learning
Example prompts
- “likelihood to respond to ICB therapies providing just the patients”
- “/bioconductor-easier”
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 Easier loads about 1.9k tokens when it runs. Until then it costs about 130 tokens; SKILL.md has 535 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 535 words (~1,851 tokens).
“This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to…”
- name
- bioconductor-easier
- when_to_use
- Use when: This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB; easier User Manual with…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/easier of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Easier 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 Easier this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.9k | Automated safety check: Pass | Custom licence | |
| tangermeme Genomic Model Analysisjmschrei/tangermeme | 318 | — | ~1.6k | Automated safety check: Pass | MIT | |
| Gtars Genomic Interval Toolkitdavila7/claude-code-templates | 33k | 11 repos | ~1.9k | Automated safety check: Pass | MIT | |
| AlphagenomeK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.4k | Automated safety check: Notes | MIT | |
| Bio Atac Seq Consensus PeaksetGPTomics/bioSkills | 1.2k | 2 repos | ~5k | Automated safety check: Pass | MIT | |
| Bio Spatial Transcriptomics Spatial PreprocessingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None |
Similar skills
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.
Alphagenome
K-Dense-AI/scientific-agent-skills
Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC…
Bio Atac Seq Consensus Peakset
GPTomics/bioSkills
Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap.
Bio Spatial Transcriptomics Spatial Preprocessing
FreedomIntelligence/OpenClaw-Medical-Skills
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data.
Bio Clip Seq M6a Clip
GPTomics/bioSkills
Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023, antibody-free chemical…
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Related
Categories
Questions about Bioconductor Easier
What does Bioconductor Easier do?
This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. Bioconductor Easier is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input.
When should I use Bioconductor Easier?
Bioconductor Easier fits situations like: tasks that involve Bioinformatics; tasks that involve Machine learning.
How do I install Bioconductor Easier in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-easier -a claude-code`. Or copy the skill folder (skills/transcriptomics/easier in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-easier in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Easier in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-easier -a codex`. Or copy the skill folder (skills/transcriptomics/easier in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-easier in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Easier 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-easier -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-easier, .gemini/skills/bioconductor-easier, .github/skills/bioconductor-easier and .opencode/skills/bioconductor-easier in your project.
What does Bioconductor Easier need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Easier is instructions for the agent only.
Does Bioconductor Easier 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 Easier 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 Easier use?
Bioconductor Easier 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 Easier use?
About 1.9k tokens (SKILL.md is roughly 7.4k 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 Easier?
Skills that share tags, products or a category with Bioconductor Easier: tangermeme Genomic Model Analysis (jmschrei/tangermeme, 318 stars), Gtars Genomic Interval Toolkit (davila7/claude-code-templates, 33k stars), Alphagenome (K-Dense-AI/scientific-agent-skills, 48k stars) and Bio Atac Seq Consensus Peakset (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Easier?
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.