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.
Run flexynesis, a deep-learning suite for multi-omics data integration and clinical outcome prediction (drug response, cancer subtyping, survival analysis).
Install Flexynesis
$ npx skills add BIMSBbioinfo/flexynesis --skill flexynesis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install BIMSBbioinfo/flexynesis flexynesis --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/BIMSBbioinfo/flexynesis.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/flexynesis .claude/skills/flexynesis && 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 "flexynesis" agent skill from https://github.com/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesis into .claude/skills/flexynesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "flexynesis", 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/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesisType 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 BIMSBbioinfo/flexynesis --skill flexynesis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install BIMSBbioinfo/flexynesis flexynesis --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BIMSBbioinfo/flexynesis.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/flexynesis .agents/skills/flexynesis && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "flexynesis" agent skill from https://github.com/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesis into .agents/skills/flexynesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "flexynesis", 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 BIMSBbioinfo/flexynesis --skill flexynesis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install BIMSBbioinfo/flexynesis flexynesis --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BIMSBbioinfo/flexynesis.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/flexynesis .cursor/skills/flexynesis && 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 "flexynesis" agent skill from https://github.com/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesis into .cursor/skills/flexynesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "flexynesis", 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/BIMSBbioinfo/flexynesis.git --path skills/flexynesis--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 BIMSBbioinfo/flexynesis --skill flexynesis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install BIMSBbioinfo/flexynesis flexynesis --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BIMSBbioinfo/flexynesis.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/flexynesis .gemini/skills/flexynesis && 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 "flexynesis" agent skill from https://github.com/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesis into .gemini/skills/flexynesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "flexynesis", 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 BIMSBbioinfo/flexynesis flexynesisInstalls 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 BIMSBbioinfo/flexynesis --skill flexynesis -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/BIMSBbioinfo/flexynesis.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/flexynesis .github/skills/flexynesis && 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 "flexynesis" agent skill from https://github.com/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesis into .github/skills/flexynesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "flexynesis", 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 BIMSBbioinfo/flexynesis --skill flexynesis -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install BIMSBbioinfo/flexynesis flexynesis --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BIMSBbioinfo/flexynesis.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/flexynesis .opencode/skills/flexynesis && 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 "flexynesis" agent skill from https://github.com/BIMSBbioinfo/flexynesis/tree/main/skills/flexynesis into .opencode/skills/flexynesis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "flexynesis", 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
flexynesis- GitHub stars
- 110
- Token cost
- ~2.3k tokens
- SKILL.md length
- 881 words
- Files
- 1
- Skills in repo
- 1
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Run flexynesis, a deep-learning suite for multi-omics data integration and clinical outcome prediction (drug response, cancer subtyping, survival analysis).
- Works in 4 steps: Get the data into the required layout → Pick a model class → Build the command → …
- The user wants to train
- SKILL.md covers Environment, Step 1: Get the data into the…, Step 2: Pick a model class and Step 3: Build the command, plus 2 more sections
- Calls mamba and pip
What it does
Flexynesis is an agent skill from BIMSBbioinfo/flexynesis. Run flexynesis, a deep-learning suite for multi-omics data integration and clinical outcome prediction (drug response, cancer subtyping, survival analysis). Use whenever the user wants to train or run inference with flexynesis, mentions multi-omics data (gene expression, CNV, methylation, mutation, proteomics, etc.) alongside a clinical/outcome prediction task, asks about integrating omics layers with deep learning, or needs to format data / build a CLI command / choose a model class / interpret outputs for…
Its SKILL.md is about 2.3k 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, Deep learning and Data pipelines and ETL. The repository describes itself as: A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner.
When your agent uses it
- The user wants to train
- Run inference with flexynesis
- Mentions multi-omics data (gene expression
- Etc.) alongside a clinical/outcome prediction task
Example prompts
- “t say”
- “by name but describes a matching task, e.g.”
- “do survival analysis combining RNA-seq and mutations.”
- “/flexynesis”
Requirements
- Python 3
Workflow steps
4 steps, taken from the step headings in SKILL.md.
- Get the data into the required layout
- Pick a model class
- Build the command
- Read the outputs
What it can do on your machine
Read from SKILL.md and the folder at commit f1305e7. 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
Shell commands in SKILL.md call:
mambapip
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):
bimsbstatic.mdc-berlin.de
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
Flexynesis loads about 2.3k tokens when it runs. Until then it costs about 186 tokens; SKILL.md has 881 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 881 words (~2,338 tokens).
“Deep learning suite for multi-omics data integration and clinical outcome prediction (drug response regression, cancer subtyping/classification, survival analysis). Published in Nature Communications (DOI: 10.1038/s41467-025-63688-5). This skill is for using flexynesis as a tool from another project — to run training/inference…”
- name
- flexynesis
Files
Just SKILL.md in skills/flexynesis of BIMSBbioinfo/flexynesis.
Open the folder on GitHubat commit f1305e7
Compare with similar skills
Flexynesis 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 |
|---|---|---|---|---|---|---|
| Flexynesis this skillBIMSBbioinfo/flexynesis | 110 | — | ~2.3k | Automated safety check: Pass | Custom licence | |
| tangermeme Genomic Model Analysisjmschrei/tangermeme | 311 | — | ~1.6k | Automated safety check: Pass | MIT | |
| Cellxgene Censusdavila7/claude-code-templates | 32k | 11 repos | ~3.8k | Automated safety check: Pass | MIT | |
| Interpro Databasegoogle-deepmind/science-skills | 3.2k | 1 repos | ~4.2k | Automated safety check: Pass | Apache-2.0 | |
| GgetK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.8k | Automated safety check: Notes | BSD-2-Clause | |
| Pixi Environment Builderxuzhougeng/wisp-science | 1k | — | ~3.7k | Automated safety check: Pass | AGPL-3.0 |
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Interpro Database
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K-Dense-AI/scientific-agent-skills
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Pixi Environment Builder
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A skill your agent uses when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels…
Bio Chipseq Motif Analysis
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Related
Categories
Questions about Flexynesis
What does Flexynesis do?
Run flexynesis, a deep-learning suite for multi-omics data integration and clinical outcome prediction (drug response, cancer subtyping, survival analysis). Flexynesis is an agent skill from BIMSBbioinfo/flexynesis. Run flexynesis, a deep-learning suite for multi-omics data integration and clinical outcome prediction (drug response, cancer subtyping, survival analysis).
When should I use Flexynesis?
Flexynesis fits situations like: the user wants to train; run inference with flexynesis; mentions multi-omics data (gene expression; etc.) alongside a clinical/outcome prediction task.
How do I install Flexynesis in Claude Code?
Run `npx skills add BIMSBbioinfo/flexynesis --skill flexynesis -a claude-code`. Or copy the skill folder (skills/flexynesis in BIMSBbioinfo/flexynesis) into .claude/skills/flexynesis in your project. Claude Code loads it when a task matches its description.
How do I install Flexynesis in Codex?
Run `npx skills add BIMSBbioinfo/flexynesis --skill flexynesis -a codex`. Or copy the skill folder (skills/flexynesis in BIMSBbioinfo/flexynesis) into .agents/skills/flexynesis in your project. Codex loads it when a task matches its description.
Can I use Flexynesis 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 BIMSBbioinfo/flexynesis --skill flexynesis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/flexynesis, .gemini/skills/flexynesis, .github/skills/flexynesis and .opencode/skills/flexynesis in your project.
What does Flexynesis need to run?
Going by SKILL.md and its folder, Flexynesis needs the command-line tools its instructions call (mamba and pip). Our summary lists: Python 3.
Does Flexynesis access the network?
SKILL.md names 1 domain. As links in the text: bimsbstatic.mdc-berlin.de. This is read from the text; nothing was executed.
Is Flexynesis 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 Flexynesis use?
Flexynesis 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 Flexynesis use?
About 2.3k tokens (SKILL.md is roughly 9.4k 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 Flexynesis?
Skills that share tags, products or a category with Flexynesis: tangermeme Genomic Model Analysis (jmschrei/tangermeme, 311 stars), Cellxgene Census (davila7/claude-code-templates, 32k stars), Interpro Database (google-deepmind/science-skills, 3.2k stars) and Gget (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 Flexynesis?
BIMSBbioinfo (a GitHub organization) maintains it in BIMSBbioinfo/flexynesis, which has 110 GitHub stars. The repository was last updated on September 9, 2026.
Source: BIMSBbioinfo/flexynesis on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.